Methods and kits for isolation and analysis of a chromatin region

ABSTRACT

The present invention encompasses methods of identifying proteins and protein modifications of proteins specifically associated with a chromatin.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the priority of U.S. provisional application No.62/014,428, filed Jun. 19, 2014, and is a continuation-in-part of U.S.application Ser. No. 14/081,812, field Nov. 15, 2013, which claims thepriority of U.S. provisional application No. 61/726,936, filed Nov. 15,2012, and U.S. provisional application No. 61/875,969, filed Sep. 10,2013, each of which is hereby incorporated by reference in its entirety.

GOVERNMENTAL RIGHTS

This invention was made with government support under R01DA025755,F32GM093614, P20RR015569, P20RR016460, U54RR020839, and UL1TR000039awarded by the National Institutes of Health. The government has certainrights in the invention.

FIELD OF THE INVENTION

The invention describes methods of identifying proteins andpost-translational modification of proteins specifically associated witha chromatin region.

BACKGROUND OF THE INVENTION

It has long been appreciated that chromatin-associated proteins andepigenetic factors play central roles in gene regulation. Mis-regulationof chromatin structure and post-translational modification of histones(PTMs) is linked to cancer and other epigenetic diseases. The field ofepigenomics has been transformed by chromatin immunoprecipitationapproaches that provide for the localization of a defined protein orpost-translationally modified protein to specific chromosomal sites.However, the hierarchy of chromatin-templated events orchestrating theformation and inheritance of different epigenetic states remains poorlyunderstood at a molecular level; there are no current methodologies thatallow for determination of all proteins present at a defined, smallregion of chromatin. Chromatin immunoprecipitation (ChIP) assays haveallowed better understanding of genome-wide distribution of proteins andhistone modifications within a genome at the nucleosome level. However,ChIP assays are largely confined to examining singular histone PTMs orproteins rather than simultaneous profiling of multiple targets, theinability to determine the co-occupancy of particular histone PTMs, andthat ChIP is reliant on the previous identification of the moleculartarget. Other chromatin immunoprecipitation methodologies do not providea mechanism for determining the specificity of protein interactions, ordo not enrich for a small integrated genomic locus and cannot detectprotein contamination in purified material. Therefore, there is a needfor methods that allow for determination of all proteins and proteinposttranslational modifications specifically associated at a defined,small region of chromatin.

SUMMARY OF THE INVENTION

In an aspect, the present invention encompasses a method of identifyingproteins, including proteins comprising posttranslational modifications,specifically associated with a target chromatin in a cell. The methodcomprises: (a) providing a first cell sample comprising nucleic acidbinding proteins and the target chromatin and a tag, wherein the targetchromatin is tagged by contacting the target chromatin with a tagcapable of specifically recognizing and binding one or more portions ofthe target chromatin and wherein the tag comprises an affinity handle,and a second cell sample comprising nucleic acid binding proteins andthe target chromatin, wherein the target chromatin is not tagged bycontacting the target chromatin with a non-functional tag that is notcapable of specifically recognizing and binding one or more portions ofthe target chromatin and wherein the non-functional tag comprises anaffinity handle; (b) isolating the affinity handle from each cell samplein (a) wherein affinity handle isolated from the first cell sampleconsists of affinity handle bound to tagged target chromatin bound tospecifically associated nucleic acid binding proteins and affinityhandle bound to non-specifically associated nucleic acid bindingproteins and affinity handle isolated from the second cell sampleconsists of affinity handle bound to non-specifically associated nucleicacid binding proteins, wherein isolating the affinity handle enrichesfor the tagged target chromatin; (c) identifying bound proteins from(b); and (d) determining the amount of each bound protein in each cellsample from (b), wherein bound proteins that are enriched in the firstcell sample as compared to the second cell sample are specificallyassociated with the tagged chromatin in the first cell sample.

BRIEF DESCRIPTION OF THE FIGURES

The application file contains at least one drawing executed in color.Copies of this patent application publication with color drawing(s) willbe provided by the Office upon request and payment of the necessary fee.

FIG. 1A-B depicts the chromatin affinity purification with massspectrometry method. (FIG. 1A) The chromatin affinity purification withmass spectrometry (ChAP-MS) approach provides for the specificenrichment of a given chromosome section and identification ofspecifically associated proteins and post-translational modifications. ALexA DNA affinity handle was engineered just upstream of the GAL1 startcodon in S. cerevisiae. Strains containing the LexA DNA binding site anda plasmid expressing LexA-PrA protein affinity handle were cultured inglucose or galactose to provide transcriptional repression oractivation, respectively, and subjected to in vivo chemical crosslinkingto trap protein interactions. Following shearing of the chromatin to˜1,000 bp, LexA-PrA was affinity purified on IgG-coated Dynabeads andcoenriched proteins/post-translational modifications were identified byhigh-resolution mass spectrometry. (FIG. 1B) To control fornonspecifically enriched proteins, a strain lacking the LexA DNA bindingsite, but containing the LexA-PrA plasmid, was cultured isotopicallyheavy (¹³C₆ ¹⁵N₂-lysine) in glucose or galactose and mixed equally withthe corresponding isotopically light culture containing the LexA DNAbinding site prior to cell lysis. Following affinity purification (AP)and mass spectrometric analysis, nonspecifically enriched proteins wereidentified as a 1:1 ratio of light to heavy lysine-containing peptides,while proteins specifically enriched with the chromosome section wereidentified with a higher level of isotopically light lysine-containingpeptides.

FIG. 2A-B depicts a plot, a Western blot image and a plot showing DNAaffinity handle for purification of a specific chromosome section. (FIG.2A) S. cerevisiae strain LEXA::GAL1 pLexA-PrA was created by insertionof a LEXA DNA binding site upstream of the GAL1 start codon viahomologous recombination. The pLexA-PrA plasmid was introduced into thisstrain and the constitutive expression of the LexA-PrA fusion proteinwas confirmed by western blotting for PrA. (FIG. 2B) Introduction of theLEXA DNA binding site does not impede GAL1 transcription. cDNA fromwild-type or LEXA::GAL1 pLexA-PrA strains grown in glucose or galactosewas used as a template for real time PCR analysis of GAL1 versus ACT1gene transcription. Error bars are the SE of triplicate analyses.

FIG. 3A-C depicts plots and a diagram showing efficiency of GAL1chromatin purification. (FIG. 3A) The effect of buffer stringency onpurification of LexA-PrA with associated chromatin was evaluated withChIP. Strain LEXA::GAL1 pLexA-PrA was subjected to ChIP using thefollowing buffer with the reagents indicated on the graph: 20 mM HEPES(pH 7.4), 0.1% Tween 20, and 2 mM MgCl₂. Enrichment of GAL1 DNA relativeto ACT1 DNA was monitored by real-time PCR. (FIG. 3B) ChIP was used tomeasure the specificity of enrichment of LexA-PrA bound chromatin.Enrichment was monitored by real-time PCR with primer sets at theindicated chromosomal locations. (FIG. 3C) GAL1 chromatin is enriched inboth glucose and galactose growth conditions. The relative efficiency ofGAL1 enrichment was monitored by real-time PCR with primers targeted tothe “0” position in panel (FIG. 3B) and to ACT1. The SE is indicated.

FIG. 4A-D depicts an image of an SDS-PAGE gel and mass spectra showingChAP-MS analysis of GAL1 chromatin. (FIG. 4A) Enrichment of GAL1chromatin under transcriptionally repressive glucose and activegalactose growth conditions. Strain LEXA::GAL1 pLexA-PrA was grown ineither glucose or galactose and subjected to affinity purification ofGAL1 chromatin via LexA-PrA as detailed in FIG. 1. Addition of anequivalent amount of isotopically heavy (¹³C₆ ¹⁵N₂-lysine) cells lackingthe LexA DNA binding site provided for the identification of proteinsspecifically enriched with GAL1 chromatin. Proteins coenriching withLexA-PrA were resolved by SDS-PAGE and visualized by Coomassie-staining.Each gel lane was sliced into 2 mm sections. Gel slices were treatedwith trypsin and resulting peptides were analyzed by high-resolutionmass spectrometry. (FIG. 4B-D) Representative high-resolution massspectra from proteins and histone post-translational modificationsidentified from the purification of transcriptionally active GAL1chromatin. (FIG. 4B) Spt16; (FIG. 4C) H3K14ac; (FIG. 4D) Rpl3(ribosomal).

FIG. 5 depicts a plot showing proteins and histone post-translationalmodifications enriched with GAL1 chromatin. Proteins and histonepost-translational modifications identified from the ChAP-MS analysis ofGAL1 chromatin in the transcriptionally active galactose and repressiveglucose growth conditions are listed in accordance to their percentisotopically light. Proteins or post-translational modifications wereconsidered specifically enriched with GAL1 chromatin if the percentisotopically light was 2 SDs from the nonspecific baseline establishedby the average of contaminant ribosomal proteins. Other proteins shownto be specifically enriched, but not correlated to gene transcription,are averaged together and listed individually in Tables 4 and 5. Thenumber of proteins averaged is shown in parentheses. The SD isindicated.

FIG. 6 depicts a plot showing the validation of proteins and histonepost-translational modifications on GAL1 chromatin. ChIP was targeted toGal3-TAP, Spt16-TAP, Rpb2-TAP, H3K14ac, and H3K36me3 undertranscriptionally active galactose and repressive glucose growthconditions. ChIP to general H3 was used as a nucleosome occupancycontrol for each histone post-translational modification ChIP.Enrichment of the 5′ end of GAL1 DNA relative to ACT1 DNA was monitoredby real-time PCR. The SE is indicated.

FIG. 7A-G depicts diagrams and graphs showing that TAL proteins canspecifically enrich native chromatin sections. (FIG. 7A) Schematicoverview of TAL-ChAP-MS technology. (FIG. 7B) A unique DNA sequence inthe promoter region of GAL1 was used to design a specific binding TALprotein that contained a PrA affinity tag. (FIG. 7C) A pTAL-PrA plasmidwas introduced into S. cerevisiae cells, and the constitutive expressionof the TAL-PrA fusion protein was confirmed by western blotting for PrA.(FIG. 7D) Expression of TAL-PrA does not impede galactose-induced GAL1transcription. cDNA from wild-type yeast and wild-type with a plasmidexpressing PrA-tagged TAL (+pTAL-PrA) grown in glucose (Glu) orgalactose (Gal) was used as a template for real time PCR analysis ofGAL1 versus ACT1 gene transcription. Error bars are the standarddeviation. (FIG. 7E-G) TAL-PrA specifically binds and enriches chromatinat the promoter of transcriptionally active GAL1. ChIP was performed tothe PrA-tag in wild-type cells containing the TAL-PrA (+pTAL-PrA, lightgray bars) and in wild-type control (dark gray bars). The efficiency ofGAL1 enrichment relative to ACT1 was monitored by real-time PCR withprimers targeted to the TAL binding site (‘0’) and to DNA sequences 2000by up- and downstream (FIG. 7E). The standard deviation is indicated.(FIG. 7F) Under transcriptionally active conditions (galactose), TAL-PrAspecifically enriched chromatin from the GAL1 promoter region relativeto sequences 2 kb up- and downstream. (FIG. 7G) The TAL-PrA protein didnot show enrichment of the GAL1 promoter chromatin undertranscriptionally repressive glucose growth conditions.

FIG. 8A-C depicts an image of an SDS-PAGE gel and graphs showingTAL-ChAP-MS analysis of GAL1 promoter chromatin from cells grown itsgalactose. (FIG. 8A) Proteins co-purifying with TAL-PrA targeted to thepromoter region of GAL1 (+pTAL-PrA lane) and proteins non-specificallyassociating with the IgG-coated Dynabeads (wild-type lane) were resolvedby SDS-PAGE/Coomassie-staining and identified by high-resolution massspectrometry. (FIG. 8B) Proteins found by label-free proteomic analysisto be enriched by >2-fold with transcriptionally active GAL1 promoterchromatin are plotted in accordance to their ranked level of enrichmentdivided by the total number of enriched proteins (N). Highlighted arethe top 10% of proteins (>15-fold enrichment) and histone PTMs enrichedwith GAL1 promoter chromatin. (FIG. 8C) ChIP was targeted to Spt16-TAP,Rpb2-TAP, Gal3-TAP and H3K14ac under transcriptionally active galactose(light gray bars) and repressive glucose (dark gray bars) growthconditions, ChIP to general H3 was used as a nucleosome occupancycontrol for H3K14ac ChIP. Enrichment adjacent to the TAL binding site inthe promoter of GAL1 relative to ACT1 was monitored by real-time qPCR.The standard error is indicated.

FIG. 9 depicts an illustration of the CRISPR-ChAP-MS approach.PrA-tagged Cas9 bound to gRNA is targeted to a specific region ofchromatin. Following chemical cross-linking, the chromatin is sheared toapproximately 1 kb in size and subjected to affinity isolation withIgG-coated beads. Isolated chromatin containing PrA-tagged Cas9/gRNA isthen analyzed with high resolution mass spectrometry to identifyspecifically associated proteins and histone posttranslationalmodifications.

FIG. 10A-C depicts a Western blot and graphs showing a PrA-taggedCas9/gRNA complex can specifically enrich a small chromatin section.(FIG. 10A) Using Western-blotting to the PrA-tag, similar expression ofPrA-Cas9 was shown in both glucose and galactose-containing media.Western-blotting to histone H4 was used as a loading control. S.cerevisiae were transformed with either a plasmid expressing PrA-taggedCas9 (pPrA-Cas9) and/or a plasmid expressing gRNA specific to a sequencein the promoter of GAL1 (pgRNA-GAL1). (FIG. 10B) Real-time reversetranscription PCR showed similar galactose-induced transcription of theGAL1 gene relative to ACT1 in cells expressing PrA-Cas9±gRNA-GAL1.Transcript levels of GAL1 are reported as a ratio of detection ingalactose relative to glucose-containing media. (FIG. 10C) PrA-Cas9/gRNAcomplex specifically enriched GAL1 promoter chromatin undertranscriptionally active conditions. Using ChIP to the PrA-tag on Cas9,enrichment at each indicated target relative to actin was measured incells containing the PrA-Cas9/gRNA complex in comparison to those withonly the PrA-Cas9. The genomic targets were: GAL1 for the genomic targetof the gRNA-GAL1, 2000 base-pairs up- and downstream of the gRNA-GAL1target, and four off-target (OT) sites for the PrA-Cas9/gRNA-GAL1complex containing varying levels of sequence similarity to thegRNA-GAL1 target (±protospacer-activation motif (PAM motif)). Error barsare standard error from triplicate analyses. (*) indicates significant(p<0.05) enrichment from galactose growths relative to glucose.

FIG. 11A-B depicts a SDS-PAGE gel and a graph showing CRISPR-ChAP-MSanalysis of transcriptionally active promoter chromatin. (FIG. 11A)Chromatin was affinity purified on IgG-beads from cells grown ingalactose-containing media that expressed PrA-Cas9 as a control andcells that expressed PrA-Cas9/gRNA targeted to the promoter region ofGAL1. Co-enriched proteins were resolved by SDS-PAGE and identified withhigh resolution mass spectrometry. Label-free proteomics was used todetermine whether a protein or histone PTM was specifically enrichedwith the promoter chromatin. (FIG. 11B) ChIP to PrA-tagged versions ofthe proteins or to the histone PTM (normalized for nucleosome occupancy)purified with the promoter chromatin was used to validate enrichment atthe GAL1 promoter relative to ACT1. Cells were grown in either glucoseor galactose-containing media.

DETAILED DESCRIPTION OF THE INVENTION

A method of isolating and identifying proteins associated with a targetregion of chromatin in a cell has been discovered. The method may alsobe used to identify post-translational modifications (PTMs) of proteinsassociated with a target chromatin in a cell. Advantageously, the methodmay be used to determine whether the association of the identifiedproteins with a chromatin in a cell is specific or non-specific. As usedherein, “specifically associated” or “specific association” of a proteinwith a target chromatin refers to any protein in a cell that normallyassociates with a chromatin in a cell. In addition, and as illustratedin the examples, the method may be used to determine the role ofproteins and post-translational modifications (PTMs) of proteins inchromatin function, including regulatory mechanisms of transcription,and the role of epigenomic factors in controlling chromatin function.

I. Method of ChAP-MS

In some aspects, the invention provides methods of isolating andidentifying proteins specifically associated with a target chromatin. Asdescribed in Example 1 and FIG. 1, a method of the invention comprisesisolating a target chromatin from a cell. As used herein, a “targetchromatin” refers to a specific chromatin or a chromatin fragment thatmay be used in an application of the invention. According to the method,isolating the target chromatin isolates nucleic acid sequences andproteins, including proteins comprising posttranslational modifications,associated with the target chromatin. The proteins and posttranslationalmodifications of proteins associated with the target chromatin may thenbe identified, and a determination of which of the identified proteinsand posttranslational modifications of proteins associated with a targetchromatin isolated from a cell are specifically or non-specificallyassociated with the target chromatin is made.

To determine which of the identified proteins and posttranslationalmodifications of proteins associated with a target chromatin isolatedfrom a cell are specifically or non-specifically associated with thetarget chromatin, a method of the invention provides two cell samples,or lysates derived from two cell samples, comprising the targetchromatin, wherein proteins in one cell sample, but not both of the cellsamples are metabolically labeled. Typically, the two cell samples aregrown identically. In addition, the target chromatin in one of the cellsamples or an extract from one of the cell samples is tagged. The twocell samples, or lysates derived from the cell samples of the inventionare combined. The tagged target chromatin is isolated in the presence ofthe other cell sample or an extract from the other cell sample.Therefore, if a target chromatin of the invention is tagged in theunlabeled cell sample, proteins specifically associated with the taggedchromatin are unlabeled, and will be isolated in the presence of labeledproteins from the labeled cell sample. Alternatively, if a targetchromatin of the invention is tagged in the labeled cell sample, theproteins associated with the tagged chromatin are labeled, and will beisolated in the presence of unlabeled proteins from the unlabeled cellsample.

As such, determining if a certain identified protein associated with thetarget chromatin is labeled, unlabeled, or a combination of labeled andunlabeled may determine if the protein was specifically associated witha target chromatin of the invention. If an identified protein comprisesa mixture of labeled and unlabeled proteins, then that protein becameassociated with a target chromatin during the chromatin isolationprocedure, and association of that protein with the target chromatin isnot specific. If a target chromatin of the invention is isolated fromthe unlabeled cell sample, only unlabeled identified proteins associatedwith the target chromatin are specifically associated with the targetchromatin. Alternatively, if a target chromatin of the invention isisolated from the labeled cell sample, only labeled identified proteinsassociated with the target chromatin are specifically associated withthe target chromatin.

In some embodiments, a tagged target chromatin of the invention isisolated from an unlabeled cell sample, and unlabeled proteinsassociated with the target chromatin are specifically associated withthe target chromatin. In other embodiments, a tagged target chromatin ofthe invention is isolated from a labeled cell sample, and labeledproteins associated with the target chromatin are specificallyassociated with the target chromatin.

(a) Cells

A target nucleic acid sequence may be isolated from any cell comprisingthe target nucleic acid sequence of the invention. A cell may be anarchaebacterium, a eubacterium, or a eukaryotic cell. For instance, acell of the invention may be a methanogen, a halophile or athermoacidophile archaeabacterium, a gram positive, a gram negative, acyanobacterium, a spirochaete, or a firmicute bacterium, a fungal cell,a moss cell, a plant cell, an animal cell, or a protist cell.

In some embodiments, a cell of the invention is a cell from an animal. Acell from an animal cell may be a cell from an embryo, a juvenile, or anadult. Suitable animals include vertebrates such as mammals, birds,reptiles, amphibians, and fish. Examples of suitable mammals includewithout limit rodents, companion animals, livestock, and primates.Non-limiting examples of rodents include mice, rats, hamsters, gerbils,and guinea pigs. Suitable companion animals include but are not limitedto cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples oflivestock include horses, goats, sheep, swine, cattle, llamas, andalpacas. Suitable primates include but are not limited to humans,capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins,spider monkeys, squirrel monkeys, and vervet monkeys. Non-limitingexamples of birds include chickens, turkeys, ducks, and geese. In someembodiments, a cell is a cell from a human.

In some embodiments, a cell may be from a model organism commonly usedin laboratory research. For instance, a cell of the invention may be anE. coli, a Bacillus subtilis, a Caulobacter crescentus, a Mycoplasmagenitalium, an Aliivibrio fischeri, a Synechocystis, or a Pseudomonasfluorescens bacterial cell; a Chlamydomonas reinhardtii, a Dictyosteliumdiscoideum, a Tetrahymena thermophila, an Emiliania huxleyi, or aThalassiosira pseudonana protist cell; an Ashbya gossypii, anAspergillus nidulans, a Coprinus cinereus, a Cunninghamella elegans, aNeurospora crassa, a Saccharomyces cerevisiae, a Schizophyllum commune,a Schizosaccharomyces pombe, or an Ustilago maydis fungal cell; anArabidopsis thaliana, a Selaginella moellendorffii, a Brachypodiumdistachyon, a Lotus japonicus, a Lemna gibba, a Zea mays, a Medicagotruncatula, a Mimulus, a tobacco, a rice, a Populus, or a Nicotianabenthamiana plant cell, a Physcomitrella patens moss; an Amphimedonqueenslandica sponge, an Arbacia punctulata sea urchin, an Aplysia seaslug, a Branchiostoma floridae deuterostome, a Caenorhabditis elegansnematode, a Ciona intestinalis sea squirt, a Daphnia spp. crustacean, aDrosophila fruit fly, a Euprymna scolopes squid, a Hydra Cnidarian, aLoligo pealei squid, a Macrostomum lignano flatworm, a Mnemiopsisleidyicomb jelly, a Nematostella vectensis sea anemone, an Oikopleuradioica free-swimming tunicate, an Oscarella carmela sponge, a Parhyalehawaiensis crustacean, a Platynereis dumerilii marine polychaetousannelid, a Pristionchus pacificus roundworm, a Schmidtea mediterraneafreshwater planarian, a Stomatogastric ganglion of various arthropodspecies, a Strongylocentrotus purpuratus sea urchin, a Symsagittiferaroscoffensis flatworm, a Tribolium castaneum beetle, a Trichoplaxadhaerens Placozoa, a Tubifex tubifex oligochaeta, a laboratory mouse, aGuinea pig, a Chicken, a Cat, a Dog, a Hamster, a Lamprey, a Medakafish, a Rat, a Rhesus macaque, a Cotton rat, a Zebra finch, a Takifugupufferfish, an African clawed frog, or a Zebrafish. In exemplaryembodiments, a cell is a Saccharomyces cerevisiae yeast cell. Inparticularly exemplary embodiments, a cell is a Saccharomyces cerevisiaeW303a yeast cell.

A cell of the invention may be derived from a tissue or from a cell linegrown in tissue culture. A cell line may be adherent or non-adherent, ora cell line may be grown under conditions that encourage adherent,non-adherent or organotypic growth using standard techniques known toindividuals skilled in the art. Cell lines and methods of culturing celllines are known in the art. Non-limiting examples of cell lines commonlycultured in a laboratory may include HeLa, a cell line from the NationalCancer Institute's 60 cancer cell lines, DU145 (prostate cancer), Lncap(prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer),PC3 (prostate cancer), T47D (breast cancer), THP-1 (acute myeloidleukemia), U87 (glioblastoma), SHSY5Y Human neuroblastoma cells, Saos-2cells (bone cancer), Vero, GH3 (pituitary tumor), PC12(pheochromocytoma), MC3T3 (embryonic calvarium), Tobacco BY-2 cells,Zebrafish ZF4 and AB9 cells, Madin-Darby canine kidney (MDCK), orXenopus A6 kidney epithelial cells.

A cell of the invention may be derived from a biological sample. As usedherein, the term “biological sample” refers to a sample obtained from asubject. Any biological sample containing a cell is suitable. Numeroustypes of biological samples are known in the art. Suitable biologicalsample may include, but are not limited to, tissue samples or bodilyfluids. In some embodiments, the biological sample is a tissue samplesuch as a tissue biopsy. The tissue biopsy may be a biopsy of a known orsuspected tumor. The biopsied tissue may be fixed, embedded in paraffinor plastic, and sectioned, or the biopsied tissue may be frozen andcryosectioned. Alternatively, the biopsied tissue may be processed intoindividual cells or an explant, or processed into a homogenate, a cellextract, a membranous fraction, or a protein extract. The sample mayalso be primary and/or transformed cell cultures derived from tissuefrom the subject. In other embodiments, the sample may be a bodilyfluid. Non-limiting examples of suitable bodily fluids include blood,plasma, serum, and urine. The fluid may be used “as is”, the cellularcomponents may be isolated from the fluid, or a protein fraction may beisolated from the fluid using standard techniques.

Suitable subjects include, but are not limited to, a human, a livestockanimal, a companion animal, a lab animal, and a zoological animal. Inone embodiment, the subject may be a rodent, e.g. a mouse, a rat, aguinea pig, etc. In another embodiment, the subject may be a livestockanimal. Non-limiting examples of suitable livestock animals may includepigs, cows, horses, goats, sheep, llamas and alpacas. In yet anotherembodiment, the subject may be a companion animal. Non-limiting examplesof companion animals may include pets such as dogs, cats, rabbits, andbirds. In yet another embodiment, the subject may be a zoologicalanimal. As used herein, a “zoological animal” refers to an animal thatmay be found in a zoo. Such animals may include non-human primates,large cats, wolves, and bears. In preferred embodiments, the animal is alaboratory animal. Non-limiting examples of a laboratory animal mayinclude rodents, canines, felines, and non-human primates. In apreferred embodiment, the subject is human.

As will be appreciated by a skilled artisan, the method of collecting abiological sample can and will vary depending upon the nature of thebiological sample and the type of analysis to be performed. Any of avariety of methods generally known in the art may be utilized to collecta biological sample. Generally speaking, the method preferably maintainsthe integrity of the sample such that chromatin can be accuratelydetected and measured according to the invention.

As described in Section (I) above, two cell samples, or lysates derivedfrom two cell samples are combined, and a tagged target chromatin of theinvention is isolated from the combined cells or combined cell lysates.Typically, cells in two cell samples of the invention are from the sametype of cells or they may be derived from the same type of cells. Forinstance, cells may comprise a heterologous nucleic acid in a targetchromatin, and may also comprise a heterologous protein expressed in acell of the invention. The heterologous nucleic acid in a targetchromatin may be used for tagging a chromatin of the invention, and theheterologous protein expressed in a cell may be used for tagging atarget chromatin as described in Section I(d). In some embodiments,cells in two cell samples of the invention are from the same type ofcells. In other embodiments, cells in the first cell sample are derivedfrom the same cell type as cells in the second cell sample.

Two cell samples of the invention may be from the same genus, species,variety or strain of cells. In preferred embodiments, two cell samplesof the invention are Saccharomyces cerevisiae yeast cells or derivativesof Saccharomyces cerevisiae yeast cells. In exemplary embodiments, twocell samples of the invention are Saccharomyces cerevisiae W303a yeastcells or derivatives of Saccharomyces cerevisiae W303a yeast cells. Inexemplary embodiments, two cell samples of the invention are derivativesof Saccharomyces cerevisiae W303a yeast cells comprising the lexAbinding site upstream of the GAL1 transcription start site, whereinprotein A is expressed in one of the cell samples of derivedSaccharomyces cerevisiae W303a yeast cells.

According to the invention, a metabolically labeled cell sample and anunlabeled cell sample are combined to generate a combined cell sample,or lysates derived from the two cell samples are combined to generate acombined cell lysate. Cell samples may be combined in a weight to weight(w/w) ratio of about 1:100 to about 100:1, about 1:50 to about 50:1,about 1:25 to about 25:1, preferably about 1:10 to about 10:1, and morepreferably about 1:5 to about 5:1. In preferred embodiments, cellsamples are combined in a w/w ratio of about 1:5 to about 5:1, about 1:2to about 2:1, about 1:1.5 to about 1.5:1, or about 1:1. In exemplaryembodiments, cell samples are combined in a w/w ratio of about 1:1. Ifcell lysates derived from two cell samples of the invention arecombined, lysates derived from cell ratios described herein arecombined. Individuals of ordinary skill in the art will recognize thatratios of cell samples or lysates derived from cell samples describedherein may be subject to statistical confidence limits of actual cellweight. For instance, the ratio may be based on 85, 90, 95% or moreconfidence limits on cell weight.

The number of cells in a cell sample can and will vary depending on thetype of cells, the abundance of a target chromatin in a cell, and themethod of protein identification used, among other variables. Forinstance, if a cell of the invention is Saccharomyces cerevisiae, about5×10¹⁰ to about 5×10¹², more preferably, about 1×10¹¹ to about 1×10¹²cells may be used in a cell sample. In some embodiments, about about1×10¹¹ to about 1×10¹² Saccharomyces cerevisiae cells are used in a cellsample.

Two cell samples of the invention are typically grown identically.Identically grown cell samples minimizes potential structural orfunctional differences at a target chromatin present in both cellsamples. As used herein, “grown identically” refers to cultured cellsamples grown using similar culture condition, or cells from a tissueharvested using identical harvesting techniques. As described below, thetwo cell samples of the invention are grown identically in a manner thatallows the metabolic labeling of proteins in one of the cell samples.For instance, the two cell samples of the invention are grownidentically, except that one of the cell samples may be grown in thepresence of a labeled amino acid as described in the examples, togenerate a cell sample with metabolically labeled proteins.

Proteins in a cell sample are metabolically labeled. Methods ofmetabolically labeling proteins in a cell are known in the art and maycomprise culturing a cell in the presence of at least one labeledanalogue of a biomolecule that is metabolized by a cell of theinvention. When the labeled analog of a biomolecule is supplied to cellsin culture instead of the unlabeled biomolecule, the labeled biomoleculeis incorporated into all newly synthesized proteins. After a number ofcell divisions, each instance of this particular labeled biomoleculewill be replaced by its labeled analog. Since there is hardly anychemical difference between the labeled biomolecule and the unlabeledbiomolecule, the cells behave exactly like the control cell populationgrown in the presence of unlabeled biomolecule. As such, up to 100% ofthe particular biomolecule in a cell may be labeled. In someembodiments, up to 10, 20, 30, 40, 50, 60, 70, 80, 90 or up to 100% ofthe particular biomolecule in a cell is labeled. In preferredembodiments, up to 50, 60, 70, 80, 90 or up to 100%, and more preferablyup to 90 or up to 100% of the particular biomolecule in a cell islabeled. In preferred embodiments, up to 100% of the particularbiomolecule in a cell is labeled.

A cell may be labeled by culturing a cell in the presence of one or morethan one labeled biomolecule. For instance, a cell may be cultured inthe presence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more labeledbiomolecules. In some embodiments, a cell may be cultured in thepresence of 1, 2, 3, 4, or 5 labeled biomolecules. In other embodiments,a cell may be cultured in the presence of 5, 6, 7, 8, 9, or 10 labeledbiomolecules. In preferred embodiments, a cell may be cultured in thepresence of 1 or 2 labeled biomolecules.

Non-limiting examples of a biomolecule that may be labeled and ismetabolized by a cell of the invention may include an amino acid, anucleic acid, a carbohydrate or a labeled molecule that may beincorporated into an amino acid, a nucleic acid, or a carbohydrate.Non-limiting examples of a labeled molecule that may be incorporatedinto an amino acid, a nucleic acid, a carbohydrate may include labeledammonium sulfate, and labeled ammonium chloride. A labeled biomoleculemay be a component of a cell culture medium such as a food source, e.g.,glucose, sera or cell extracts. In some embodiments, a labeledbiomolecule that is metabolized by a cell of the invention is a labelednucleic acid. In other embodiments, a labeled biomolecule that ismetabolized by a cell of the invention is a labeled carbohydrate such as[¹³C]glucose.

In preferred embodiments, a biomolecule that is metabolized by a cell ofthe invention is a labeled amino acid. In general, a labeled amino acidof the invention may be a labeled L-amino acid, a labeled D-amino acidor a mixture thereof. In preferred embodiments, a labeled amino acids isa labeled L-amino acids. A labeled amino acid may be a free amino acidor an amino acid salt. A labeled amino acid may also be in the form ofintact protein or peptide, provided that the protein or peptidecomprises a labeled amino acid of the invention. In some preferredembodiments, a labeled amino acid that may be used for metabolicallylabeling a cell of the invention may be a labeled L-Lysine, L-Arginine,L-Methionine, L-Tyrosine, or combinations thereof.

A labeled biomolecule may be labeled using a heavy isotope of one ormore atoms of the biomolecule. Non limiting examples of a heavy isotopeof one or more atoms of a biomolecule may include heavy hydrogen,carbon, nitrogen, phosphorous, oxygen, or sulfur. A labeled biomoleculemay be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1718, 19 or 20 Da or more heavier than an unlabeled biomolecule. In someembodiments, a labeled biomolecule is about 1, 2, 3, 4, or 5 Da heavierthan an unlabeled biomolecule. In other embodiments, a labeledbiomolecule is about 5, 6, 7, 8, 9, or 10 Da heavier than an unlabeledbiomolecule. In yet other embodiments, a labeled biomolecule is about10, 11, 12, 13, 14, or 15 Da heavier than an unlabeled biomolecule. Inadditional embodiments, a labeled biomolecule is about 15, 16, 17 18, 19or 20 Da heavier than an unlabeled biomolecule. In preferredembodiments, a labeled biomolecule is about 4, 5, 6, 7, 8, 9, or 10 Daheavier than an unlabeled biomolecule.

In preferred embodiments, a labeled biomolecule is a labeled amino acidthat may be used for metabolically labeling a cell of the invention maybe a heavy analog of L-Lysine, L-Arginine, L-Methionine, L-Tyrosine, orcombinations thereof. Non limiting examples of heavy analogs ofL-Lysine, L-Arginine, L-Methionine, L-Tyrosine may include,[¹³C₆]-L-Lysine, [¹³C₆, ¹⁵N₂]-L-Lysine, [¹³C₆, ¹⁵N₂, D9]-L-Lysine,[¹⁵N₂, D9]-L-Lysine, [4,4,5,5-D4]-L-Lysine, [¹⁵N₂]-L-Lysine, [¹³C₆,¹⁵N₂]-L-Lysine, [¹³C₆]-L-Arginine, [U—¹³C₆, ¹⁵N₄]-L-Arginine, [U—¹³C₆,¹⁵N₄, D7]-L-Arginine, [¹⁵N₄, D7]-L-Arginine, [¹⁵N₄]-L-Arginine, [¹³C₆,¹⁵N₄]-L-Arginine, [1-13C, methyl-D3]-L-Methionine, [¹³C₉; 9Da]-L-Tyrosine, [¹⁵N]-L-Tyrosine, and [¹³C₉, ¹⁵N]-L-Tyrosine. In anexemplary embodiment, a labeled amino acid used to metabolically label acell of the invention is [¹³C6, ¹⁵N4]-L-Arginine.

(b) Chromatin

A method of the invention comprises identification of a protein andpost-translational modification of a protein associated with a targetchromatin. Generally, chromatin refers to the combination of nucleicacids and proteins in the nucleus of a eukaryotic cell. However, it iscontemplated that the term “chromatin” may also refer to the combinationof any nucleic acid sequence and proteins associated with the nucleicacid sequence in any cell.

A chromatin of the invention may comprise single stranded nucleic acid,double stranded nucleic acid, or a combination thereof. In someembodiments, a chromatin comprises single stranded nucleic acid. Inother embodiments, a chromatin comprises a combination of singlestranded and double stranded nucleic acids. In yet other embodiments, achromatin comprises double stranded nucleic acid.

A chromatin of the invention may comprise a ribonucleic acid (RNA), adeoxyribonucleic acid (DNA), or a combination of RNA and DNA. In someembodiments, a chromatin of the invention comprises a combination of aRNA sequence and proteins associated with the RNA sequence in a cell.Non-limiting examples of RNA sequences may include mRNA, and non-codingRNA such as tRNA, rRNA, snoRNAs, microRNAs, siRNAs, piRNAs and the longnoncoding RNA (lncRNA). In preferred embodiments, a chromatin of theinvention comprises a combination of a DNA sequence and proteinsassociated with the DNA sequence in a cell. In other preferredembodiments, a chromatin of the invention comprises a combination of RNAand DNA sequences, and proteins associated with the RNA and DNA sequencein a cell. Non limiting examples of chromatin that may comprise acombination of RNA and DNA may include genomic DNA undergoingtranscription, or genomic DNA comprising non-coding RNA such as lncRNA.

A chromatin of the invention may be genomic chromatin such as, chromatinfrom a chromosome of a cell, or chromatin from an organelle in the cell.Alternatively, a chromatin may be chromatin from an extrachromosomalnucleic acid sequence. In some embodiments, a chromatin of the inventionis chromatin from an organelle in the cell. Non-limiting examples of achromatin from an organelle may include mitochondrial nucleic acidsequence in plant and animal cells, and a chloroplast nucleic acidsequence in plant cells. In some embodiments, a nucleic acid sequence ofthe invention is a mitochondrial nucleic acid sequence. In otherembodiments, a nucleic acid sequence of the invention is a chloroplastnucleic acid sequence.

In some embodiments, a chromatin of the invention is chromatin from anextrachromosomal nucleic acid sequence. The term “extrachromosomal,” asused herein, refers to any nucleic acid sequence not contained withinthe cell's genomic nucleic acid sequence. An extrachromosomal nucleicacid sequence may comprise some sequences that are identical or similarto genomic sequences in the cell, however, an extrachromosomal nucleicacid sequence as used herein does not integrate with genomic sequencesof the cell. Non-limiting examples of an extrachromosomal nucleic acidsequence may include a plasmid, a virus, a cosmid, a phasmid, and aplasmid.

In some preferred embodiments, a chromatin of the invention is genomicchromatin. In exemplary embodiments, a chromatin of the invention isgenomic chromatin of a eukaryotic cell. A eukaryotic cell of theinvention may be as described in Section I(a) above.

Primary functions of genomic chromatin of a eukaryotic cell may be DNApackaging into a smaller volume to fit in the cell, strengthening of theDNA to allow mitosis, prevent DNA damage, and to control gene expressionand DNA replication. As described above, genomic chromatin of aeukaryotic cell may comprise DNA sequences and a plurality ofDNA-binding proteins as well as certain RNA sequences, assembled intohigher order structural or functional regions. As used herein, a“structural or functional feature of a chromatin”, refers to a chromatinfeature characterized by, or encoding, a function such as a regulatoryfunction of a promoter, terminator, translation initiation, enhancer,etc., or a structural feature such as heterochromatin, euchromatin, anucleosome, a telomere, or a centromere. A physical feature of a nucleicacid sequence may comprise a functional role and vice versa. Asdescribed below, a chromatin of the invention may be a chromatinfragment, and as such may comprise a fragment of a physical orfunctional feature of a chromatin, or no physical or functional featuresor known physical or functional features.

The primary protein components of genomic eukaryotic chromatin arehistones that compact the DNA into a nucleosome. The nucleosomecomprises an octet of histone proteins around which is wound a stretchof double stranded DNA sequence of about 150 to about 250 bp in length.Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1may act to link adjacent nucleosomes together into a higher orderstructure. Histones are subject to post translational which may affecttheir function in regulating chromatin function. Such modifications mayinclude methylation, citrullination, acetylation, phosphorylation,SUMOylation, ubiquitination, and ADP-ribosylation.

Many further polypeptides and protein complexes interact with thenucleosome and the histones to regulate chromatin function. A“polypeptide complex” as used herein, is intended to describe proteinsand polypeptides that assemble together to form a unitary association offactors. The members of a polypeptide complex may interact with eachother via non-covalent or covalent bonds. Typically members of apolypeptide complex will cooperate to enable binding either to a nucleicacid sequence or to polypeptides and proteins already associated with orbound to a nucleic acid sequence in chromatin. Chromatin associatedpolypeptide complexes may comprise a plurality of proteins and/orpolypeptides which each serve to interact with other polypeptides thatmay be permanently associated with the complex or which may associatetransiently, dependent upon cellular conditions and position within thecell cycle. Hence, particular polypeptide complexes may vary in theirconstituent members at different stages of development, in response tovarying physiological conditions or as a factor of the cell cycle. Byway of example, in animals, polypeptide complexes with known chromatinremodelling activities include Polycomb group gene silencing complexesas well as Trithorax group gene activating complexes.

Additionally, a protein associated with a chromatin of the invention maybe a protein normally expressed in a cell, or may be an exogenousheterologous protein expressed in a cell. In some embodiments, a proteinassociated with a chromatin of the invention is a protein normallyexpressed in a cell. In other embodiments, a protein associated with achromatin of the invention is a protein not normally expressed in acell.

A chromatin of the invention may be an intact and complete chromatinfrom the cell, or may be a fragment of a chromatin in a cell. In someembodiments, a chromatin of the invention is an intact chromatinisolated from a cell. For instance, a chromatin of the invention may bea plasmid, a cosmid, or a phage chromatin or a complete organellarchromatin. In preferred embodiments, a chromatin of the invention is afragment of a chromatin from a cell. In exemplary embodiments, achromatin of the invention is a fragment of a genomic chromatin from acell.

When a chromatin of the invention is a fragment of a chromatin in acell, any method of fragmenting a chromatin known in the art may beused. Such methods may include physical methods of fragmenting achromatin, or enzymatic digestion of a nucleic acid sequence of achromatin. In some embodiments, a fragment of a chromatin may begenerated using enzymatic digestion of a nucleic acid sequence inchromatin. Non-limiting examples of enzymatic digestion may includerandom or sequence specific enzymatic digestion using restrictionenzymes, nucleases, combinations of restriction enzymes and nucleases,or combinations of nicking and other nucleases such as NEBNext™fragmentase, which comprises a nicking enzyme that randomly generatesnicks in double stranded DNA and another enzyme that cuts the strandopposite to the generated nicks.

In other embodiments, a fragment of a chromatin may be generated using aphysical method of fragmenting a chromatin. Non-limiting examples ofphysical fragmenting methods that may be used to fragment a chromatin ofthe invention may include nebulization, sonication, and hydrodynamicshearing. In some embodiments, a fragment of a chromatin may begenerated using nebulization. In other embodiments, a fragment of achromatin may be generated using hydrodynamic shearing. In preferredembodiments, a fragment of a chromatin may be generated usingsonication. During sonication, a sample comprising chromatin issubjected to ultrasonic waves, whose vibrations produce gaseouscavitations in the liquid that shear or break high molecular weightmolecules such as chromatin through resonance vibration. Sonicationmethods that may be used to generate a chromatin of the invention areknown in the art

A fragment of a chromatin of the invention may comprise a nucleic acidsequence fragment and may be about 10, 50, 100, 150, 200, 250, 300, 350,400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050,1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650,1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, 2250,2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850,2900, 2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000bases long or more. In some embodiments, a chromatin of the inventionmay comprise a nucleic acid sequence fragment of about 10, 20, 30, 40,50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190,200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330,340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470,480, 490, or about 500 bases long. In other embodiments, a chromatin ofthe invention may comprise a nucleic acid sequence fragment of about500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630,640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, or about 1000 bases long. In yetother embodiments, a chromatin of the invention may comprise a nucleicacid sequence fragment of about 1000, 1010, 1020, 1030, 1040, 1050,1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170,1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290,1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400, 1410,1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500 baseslong. In other embodiments, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1500, 1510, 1520, 1530, 1540,1550, 1560, 1570, 1580, 1590, 1600, 1610, 1620, 1630, 1640, 1650, 1660,1670, 1680, 1690, 1700, 1710, 1720, 1730, 1740, 1750, 1760, 1770, 1780,1790, 1800, 1810, 1820, 1830, 1840, 1850, 1860, 1870, 1880, 1890, 1900,1910, 1920, 1930, 1940, 1950, 1960, 1970, 1980, 1990, or about 2000bases long. In additional embodiments, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 2000, 2100, 2150,2200, 2250, 2300, 2350, 2400, 2450, or about 2500 bases long. In otherembodiments, a chromatin of the invention may comprise a nucleic acidsequence fragment of about 2000, 2050, 2100, 2150, 2200, 2250, 2300,2350, 2400, 2450, or about 2500 bases long. In still other embodiments,a chromatin of the invention may comprise a nucleic acid sequencefragment of about 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900,2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000 baseslong or more.

In some preferred embodiments, a chromatin fragment of the invention maycomprise a nucleic acid sequence fragment of about 550, 560, 570, 580,590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720,730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860,870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120,1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240,or about 1250 bases long. In a preferred embodiment, a chromatin of theinvention may comprise a nucleic acid sequence fragment of about 750,760, 770, 780, 790, 800, 810, 820, 830, 840, or about 850 bases long. Inanother preferred embodiment, a chromatin of the invention may comprisea nucleic acid sequence fragment of about 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, or about 1050 bases long.

In other preferred embodiments, a chromatin fragment of the inventionmay comprise a nucleic acid sequence fragment of about 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040,1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160,1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280,1290, 1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400,1410, 1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500bases long. In a preferred embodiment, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 950, 960, 970, 980,990, 1000, 1010, 1020, 1030, 1040, or about 1050 bases long. In anotherpreferred embodiment, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1200, 1210, 1220, 1230, 1240,1250, 1260, 1270, 1280, 1290, or about 1300 bases long.

As described in this section above, a chromatin of the invention maycomprise one or more nucleosomes. As such, a chromatin fragment of theinvention may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, or about 20 nucleosomes. In some embodiments, achromatin fragment of the invention may comprise about 1, 2, 3, 4, orabout 5 nucleosomes. In other embodiments, a chromatin fragment of theinvention may comprise about 5, 6, 7, 8, 9, or about 10 nucleosomes. Inyet other embodiments, a chromatin fragment of the invention maycomprise about 10, 11, 12, 13, 14, or about 15 nucleosomes. In otherembodiments, a chromatin fragment of the invention may comprise about15, 16, 17, 18, 19, or about 20 nucleosomes. In preferred embodiments, achromatin fragment of the invention may comprise about 4 nucleosomes. Inother preferred embodiments, a chromatin fragment of the invention maycomprise about 5 nucleosomes.

A target chromatin fragment of the invention may comprise a structuralor a functional feature of chromatin as described above, a fragment of aphysical or functional feature, or no physical or functional features orknown physical or functional features. In some embodiments, a targetchromatin fragment of the invention comprises a structural feature ofchromatin. In other embodiments, a target chromatin fragment of theinvention comprises no physical or functional features or known physicalor functional features. In yet other embodiments, a target chromatinfragment of the invention comprises a functional feature of chromatin.In exemplary embodiments, a functional feature of chromatin is apromoter. In particularly exemplary embodiments, a functional feature ofchromatin is a GAL1 promoter of Saccharomyces cerevisiae.

(c) Preparation of Cell Lysate

A target chromatin is isolated from a combined cell lysate. A combinedcell lysate comprises a lysate of two combined cell samples, or acombination of two cell lysates derived from two cell samples, wherein atarget chromatin is tagged in one of the cell samples. Irrespective ofwhether one cell sample or a combined cell sample is lysed, a skilledpractitioner of the art will appreciate that structural and functionalfeatures of a target chromatin must be preserved during cell lysis andisolation of the target chromatin. The association of proteins with atarget chromatin may be preserved during cell lysis and isolation of thetarget chromatin using methods known in the art for preserving a complexof proteins with a nucleic acid sequence. For instance, lysing of a celland isolation of a target chromatin may be performed under refrigerationor using cryogenic methods and buffer conditions capable of preservingassociation of proteins and nucleic acid sequences. In addition, acomplex of proteins with a nucleic acid may be preserved by crosslinkingprotein and nucleic acid complexes in a cell prior to lysing andisolating a chromatin. Crosslinking protein and nucleic acid complexesin a cell may also capture, or preserve, transient protein-protein andprotein-nucleic acid interactions.

In some embodiments, a complex of proteins with a nucleic acid may bepreserved by crosslinking protein and nucleic acid complexes in achromatin prior to lysing a cell and isolating the chromatin.Crosslinking is the process of joining two or more molecules such as twoproteins or a protein and a nucleic acid molecule, by a covalent bond.Molecules may be crosslinked by irradiation with ultraviolet light, orby using chemical crosslinking reagents. Chemical crosslinking reagentscapable of crosslinking proteins and nucleic acids are known in the artand may include crosslinking reagents that target amines, sulfhydryls,carboxyls, carbonyls or hydroxyls; omobifunctional or heterobifunctionalcrosslinking reagent, variable spacer arm length or zero-lengthcrosslinking reagents, cleavable or non-cleavable crosslinking reagents,and photoreactive crosslinking reagents. Non-limiting examples ofcrosslinking reagents that may be used to crosslink protein complexesand/or protein complexes and nucleic acids may include formaldehyde,glutaraldehyde, disuccinimidyl glutarate, disuccinimidyl suberate, aphotoreactive amino acid such as photo-leucine or photo-methionine, andsuccinimidyl-diazirine. The degree of crosslinking can and will varydepending on the application of a method of the invention, and may beexperimentally determined.

In a preferred embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehyde.In an exemplary embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehydeas described in the examples.

A skilled practitioner of the art will appreciate that protocols forlysing a cell can and will vary depending on the type of cell, thetarget chromatin of the invention, and the specific application of amethod of the invention. Non limiting examples of methods that may beused to lyse a cell of the invention may include cell lysis using adetergent, an enzyme such as lysozyme, incubation in a hypotonic bufferwhich causes a cell to swell and burst, mechanical disruption such asliquid homogenization by forcing a cell through a narrow space,sonication, freeze/thaw, mortar and pestle, glass beads, andcombinations thereof. In some embodiments, when a cell of the inventionis a yeast cell, the cell may be cryogenically lysed under liquidnitrogen temperature with glass beads. In exemplary embodiments, when acell of the invention is a yeast cell, the cell may be cryogenicallylysed under liquid nitrogen temperature with glass beads as described inthe examples.

Buffer conditions used during lysing and isolation of a chromatin of theinvention can and will be altered to control stringent conditions duringcell lysis and isolation to preserve association of proteins and nucleicacid sequences of a chromatin. “Stringent conditions” in the context ofchromatin isolation are conditions capable of preserving specificassociation of proteins and nucleic acids of a chromatin, but minimizingnon-specific association of proteins and nucleic acids. Stringentcondition can and will vary depending on the application of a method ofthe invention, the target chromatin of the invention, the nucleic acidsequence in a target chromatin, the proteins or protein complexesassociated with a target chromatin of the invention, whether or notproteins, protein complexes and nucleic acid sequences are crosslinked,and the conditions used for crosslinking proteins, protein complexes andnucleic acid sequences of a target chromatin. For instance, morestringent buffer conditions may be used in a method of the inventionwherein proteins, protein-protein complexes, and protein-nucleic acidcomplexes are crosslinked compared to a method of the invention whereinproteins, protein-protein complexes, and protein-nucleic acid complexesare not crosslinked. As such, stringent buffer conditions used duringcell lysis and isolation of a nucleic acid sequence of the invention maybe experimentally determined for each application wherein a method ofthe invention is used. Buffer conditions that may alter stringentconditions during cell lysis and isolation may include pH and saltconcentration. In preferred embodiments, proteins, protein-proteincomplexes, and protein-nucleic acid complexes of a target chromatin ofthe invention are crosslinked, and stringent buffer conditions are usedduring lysis and isolation of a chromatin of the invention. In exemplaryembodiments, proteins, protein-protein complexes, and protein-nucleicacid complexes of a target chromatin of the invention are crosslinked,and stringent buffer conditions are used during lysis and isolation of achromatin of the invention and are as described in the examples.

(d) Chromatin Isolation

According to the invention, a tagged target chromatin is isolated from acombined cell lysate. As described in Sections I(a) and I(c) above, acombined cell lysate comprises a lysate of two combined cell samples, ora combination of two cell lysates derived from two cell samples, whereina target chromatin is tagged in one of the lysates, or one of the cellsamples. As such, a target chromatin is isolated from a cell lysatecomprising a combination of a tagged target chromatin and an untaggedtarget chromatin. The ratio of tagged target chromatin to untaggedtarget chromatin reflects the ratio at which the two cell samples or thelysates derived from the two cell sample are combined. In addition,proteins in one of the cell samples or lysate derived from one of thecell samples are metabolically labeled. Therefore, when a tagged targetchromatin is from a cell sample wherein proteins are metabolicallylabeled, a cell lysate of the invention comprises a combination of atagged target chromatin comprising metabolically labeled proteins, andan untagged target chromatin comprising unlabeled proteins. Conversely,when a tagged target chromatin is from a cell sample wherein proteinsare unlabeled, a cell lysate of the invention comprises a combination ofa tagged target chromatin comprising unlabeled proteins, and an untaggedtarget chromatin comprising labeled proteins.

A target chromatin may be isolated from a mixture of chromatins orchromatin fragments in a cell lysate as described in this section. Asused herein, a target nucleic acid sequence is said to be “isolated” or“purified” when it is substantially free of proteins not associated withthe target chromatin, nucleic acid sequences other than the nucleic acidsequences associated with the target chromatin, and other cell debrisand cell contents resulting from extraction and preparation of thetarget chromatin from a cell. A target chromatin of the presentinvention may be purified to homogeneity or other degrees of purity. Ingeneral, the level of purity of an isolated target chromatin can andwill vary depending on the cell type, the specific chromatin to beisolated, and the intended use of a target chromatin of the invention.The level of purity of an isolated target chromatin may be determinedusing methods known in the art. For instance, the level of purity of anisolated target chromatin may be determined by determining the level ofpurity of a nucleic acid sequence associated with a target chromatin, bydetermining the level of purity of a protein associated with a targetchromatin, or by determining the level of enrichment of a targetchromatin, compared to a non-target chromatin in a cell. In preferredembodiments, the level of purity of an isolated target chromatin isdetermined by determining the level of enrichment of a target chromatin,compared to a non-target chromatin in a cell. Determining the level ofenrichment of a target chromatin, compared to a non-target chromatin ina cell may be as described in this section below.

A target chromatin of the invention may be isolated using methods knownin the art, such as electrophoresis, molecular, immunological andchromatographic techniques, ion exchange, hydrophobic, affinity, andreverse-phase HPLC chromatography, size exclusion chromatography,precipitation, dialysis, chromatofocusing, ultrafiltration anddiafiltration techniques, and combinations thereof. For general guidancein suitable purification techniques, see Scopes, R., ProteinPurification, Springer-Vertag, NY (1982).

In general, a method of the invention comprises isolating a targetchromatin by affinity purification, or affinity purification incombination with other methods of isolating chromatin described above.In a preferred embodiment, a method of the invention comprises isolatinga target chromatin by affinity purification. Non limiting examples ofaffinity purification techniques that may be used to isolate a targetchromatin of the invention may include affinity chromatography,immunoaffinity chromatography, size exclusion chromatography, andcombinations thereof. See, for example, Roe (ed), Protein PurificationTechniques: A Practical Approach, Oxford University Press, 2nd edition,2001.

In essence, affinity purification of a target chromatin may comprisetagging a target chromatin by contacting the target chromatin of theinvention with a tag capable of specifically recognizing and binding oneor more portions of a target chromatin. As used herein, “specificallyrecognizing” refers to a binding reaction between two separate moleculesthat is at least two times the background and more typically more than10 to 100 times the background molecular associations underphysiological conditions. As described in Section (I), two cell samples,or lysates derived from the cell samples of the invention are combined,and a target chromatin in one of the cell samples or an extract from oneof the cell samples is tagged. In addition, proteins in one cell sample,but not both of the cell samples are metabolically labeled. As such, atarget chromatin may be tagged in a cell or an extract from a cellwherein proteins are metabolically labeled, and proteins specificallyassociated with an isolated target chromatin are metabolically labeled.Alternatively, a target chromatin may be tagged in a cell or an extractfrom a cell wherein proteins are not metabolically labeled, and proteinsspecifically associated with an isolated target chromatin are notmetabolically labeled. In some embodiments, a target chromatin is taggedin a cell or an extract from a cell wherein proteins are metabolicallylabeled. In other embodiments, a target chromatin is tagged in a cell oran extract from a cell wherein proteins are metabolically labeled.

A tag may be capable of specifically recognizing and binding 1, 2, 3, 4,5, 6, 7, 8, 9, or 10 components of a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and bindingone component of a target chromatin.

A tag may be capable of specifically recognizing and binding a componentin a target chromatin. A component in a target chromatin may be anucleic acid sequence in a nucleic acid associated with a targetchromatin, a protein associated with a target chromatin, or a chromatinstructural or functional feature in a target chromatin. In someembodiments, a tag is capable of specifically recognizing and binding aprotein associated with a target chromatin. In other embodiments, a tagis capable of specifically recognizing and binding a chromatinstructural or functional feature in a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and binding anucleic acid sequence associated with a target chromatin.

A nucleic acid sequence associated with a target chromatin that may bespecifically recognized and bound by a tag of the invention may be anucleic acid sequence normally found in a chromatin of a cell of theinvention. Alternatively, a nucleic acid sequence associated with atarget chromatin that may be specifically recognized and bound by a tagof the invention may be an exogenous nucleic acid sequence introducedinto a cell to facilitate tagging a target chromatin of the invention.In some embodiments, a nucleic acid sequence that may be recognized andbound by a tag is a nucleic acid sequence normally found in a chromatinof a cell of the invention. In other embodiments, a nucleic acidsequence that may be recognized and bound by a tag of the invention isan exogenous nucleic acid sequence introduced into a cell of theinvention to facilitate tagging a chromatin of the invention. Nonlimiting examples of an exogenous nucleic acid sequence introduced intoa cell to facilitate tagging a target chromatin of the invention may bethe lexA binding sequence, and the Lac operator. In a preferredembodiment, a heterologous nucleic acid sequence introduced into a cellto facilitate tagging a target nucleic acid sequence of the invention isthe lexA binding sequence. In an exemplary embodiment, a heterologousnucleic acid sequence introduced into a cell to facilitate tagging atarget nucleic acid sequence of the invention is the lexA bindingsequence immediately upstream of the transcription start site.

Individuals of ordinary skill in the art will recognize that anexogenous chromatin component introduced into a cell to facilitatetagging a target chromatin of the invention cannot and will not disrupta target chromatin, or a structural or functional feature of a targetchromatin. Methods of designing a chromatin component and a tag capableof binding the chromatin component that do not disrupt a chromatin ofthe invention may depend on the particular application of a method ofthe invention, and may be determined experimentally. For instance, if anapplication of a method of the invention comprises promoter function, atag may be designed to bind anywhere adjacent to the promoter, butwithout disrupting the promoter.

A tag of the invention may further comprise one or more affinityhandles. As used herein, the term “affinity handle” may refer to anyhandle that may be bound by a substrate for affinity purification, asdescribed below. A tag may comprise one or more than one affinityhandle. The inclusion of more than one affinity handle in a tag of theinvention may significantly increase the efficiency of affinitypurification for a low copy number chromatin target. As such, a tag mayfurther comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more affinity handles.In a preferred embodiment, a tag of the invention comprises one affinityhandle.

Affinity handles may include any affinity handle for which a cognatebinding agent is readily available. An affinity handle may be anaptamer, an antibody, an antibody fragment, a double-stranded DNAsequence, modified nucleic acids and nucleic acid mimics such as peptidenucleic acids, locked nucleic acids, phosphorodiamidate morpholinooligomers (PMO), a ligand, a ligand fragment, a receptor, a receptorfragment, a polypeptide, a peptide, a coenzyme, a coregulator, anallosteric molecule, non-immunoglobulin scaffolds such as Affibodies,Anticalins, designed Ankyrin repeat proteins and others, an ion, or asmall molecule for which a cognate binding agent is readily available.The term “aptamer” refers to a polypeptide or a polynucleotide capableof binding to a target molecule at a specific region. It is generallyaccepted that an aptamer, which is specific in its binding to anypolypeptide, may be synthesized and/or identified by in vitro evolutionmethods. Non limiting examples of handles that may be suitable forisolating a chromatin may include biotin or a biotin analogue such asdesthiobiotin, digoxigenin, dinitrophenol or fluorescein, amacromolecule that binds to a nucleic acid or a nucleic acid bindingprotein such as the Lac repressor, a zinc finger protein, atranscription activator protein capable of binding a nucleic acid, or atranscription activator-like (TAL) protein, antigenic polypeptides suchas protein A, or peptide ‘tags’ such as polyhistidine, FLAG, HA and Myctags. In preferred embodiments, a tag of the invention comprises anantigenic polypeptide. In exemplary embodiments, a tag of the inventioncomprises the protein A antigenic polypeptide, or derivatives thereof.Protein A is capable of binding the lexA binding site, and comprises anaffinity handle capable of binding IgG. As such, protein A may be usedas an affinity purification tag for purifying a target chromatincomprising a lexA binding tag.

In some embodiments, a tag of the invention is a nucleic acid tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin isintroduced into a cell of the invention. In some embodiments, a tag ofthe invention is a nucleic acid tag capable of binding a nucleic acidsequence component of a chromatin, wherein the nucleic acid sequencecomponent of the chromatin is normally present in a cell of theinvention. Non-limiting examples of nucleic acid tags capable of bindinga nucleic acid sequence component of a chromatin include antisense RNAor DNA nucleic acid tags, and tags comprising modified nucleic acids andnucleic acid mimics such as peptide nucleic acids, locked nucleic acids,phosphorodiamidate morpholino oligomers (PMO). In some embodiments, atag of the invention is a nucleic acid tag comprising lockednucleotides. For instance, a nucleic acid tag comprising lockednucleotides may be as described in US20110262908 or US20120040857, and apeptide nucleic acid tag may be as described in Boffa et al. 1995 PNAS92:1901-1905, the disclosures of all of which are incorporated herein intheir entirety.

In some preferred embodiments, a tag of the invention is a protein tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin is anucleic acid sequence normally found in a chromatin of a cell of theinvention. Non limiting examples of a protein tag capable of binding anucleic acid sequence normally found in a chromatin of a cell may be anucleic acid binding protein such as protein A, the Lac repressor, azinc finger protein, a transcription activator protein capable ofbinding a nucleic acid, or a transcription activator-like (TAL) protein.In one embodiment, a tag of the invention is a transcription activatorprotein capable of binding a nucleic acid sequence normally found in achromatin of a cell of the invention. In another embodiment, a tag ofthe invention is a zinc finger protein capable of binding a nucleic acidsequence normally found in a chromatin of a cell of the invention. Inyet another embodiment, a tag of the invention is a transcriptionactivator-like (TAL) protein capable of binding a nucleic acid sequencenormally found in a chromatin of a cell of the invention.

A nucleic acid binding protein tag of the invention may be a wild typenucleic acid binding protein capable of binding a nucleic acid sequencenormally found in a target chromatin. Alternatively, a nucleic acidbinding protein tag of the invention may be engineered to have bindingspecificity for a nucleic acid sequence component normally found in atarget chromatin of the invention. Individuals of ordinary skill in theart will recognize that nucleic acid binding proteins such as zincfinger proteins, transcription activator proteins, and transcriptionactivator-like (TAL) proteins may be engineered to have novel nucleicacid binding specificity compared to naturally-occurring forms of theproteins. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, andU.S. Pate. Appl. Nos 20110239315, 20120110685, and 20120270273, thedisclosures of which are incorporated by reference herein in theirentireties. In some embodiments, a nucleic acid binding protein tag ofthe invention is a wild type nucleic acid binding protein capable ofbinding a nucleic acid sequence normally found in a target chromatin. Inother embodiments, a nucleic acid binding protein tag of the inventionis a nucleic acid binding protein engineered to have binding specificityfor a nucleic acid sequence component of a target chromatin of theinvention. In a preferred embodiment, a nucleic acid binding protein tagof the invention is a zinc finger protein engineered to have bindingspecificity for a nucleic acid sequence component of a target chromatinof the invention. In another preferred embodiment, a nucleic acidbinding protein tag of the invention is a TAL protein engineered to havebinding specificity for a nucleic acid sequence component of a targetchromatin of the invention.

In other preferred embodiments, a tag of the invention is a protein tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin is anexogenous nucleic acid sequence introduced into a cell of the invention.In exemplary embodiments, a tag of the invention is a protein A tagcapable of binding the lexA exogenous nucleic acid sequence introducedin a cell of the invention. In an exemplary embodiment, a tag of theinvention is a protein A tag capable of binding the lexA exogenousnucleic acid sequence introduced upstream of the transcriptional startsite of the GAL1 promoter of a S. cereviseae cell as described in theexamples.

A target chromatin may be contacted with a tag at any time during amethod of the invention leading to isolation of target chromatin. Forinstance, a target chromatin may be contacted with a protein tag duringcell culture by expressing the protein tag in a cell of the invention.Alternatively, a target chromatin may be contacted with a tag after cellculture but before cell lysis, after cell lysis, or after fragmentationof chromatin to generate chromatin fragments comprising a targetchromatin.

In some embodiments, a target chromatin is contacted with a tag aftercell culture but before cell lysis. As such, a tag may be introducedinto a cell before cell lysis. Methods of introducing a tag into a cellof the invention can and will vary depending on the type of cell, thetag, and the application of a method of the invention. For instance, anucleic acid tag may be electroporated into a cell after culture. Inother embodiments, a target chromatin is contacted with a tag after celllysis. In such an embodiment, a tag may be added to the cell lysate as arecombinant protein. The recombinant protein may be expressed, isolatedand purified via methods standard in the art for protein purification.In yet other embodiments, a target chromatin is contacted with a tagafter cell lysis and chromatin fragmentation. In preferred embodiments,a target chromatin is contacted with a tag during cell culture byexpressing the tag in a cell of the invention during cell culture. Inexemplary embodiments, a target chromatin comprises the lexA bindingsite, and the lexA binding site is contacted with a protein A tag duringcell culture by expressing the protein A in a cell of the inventionduring cell culture. In an exemplary embodiment, a target chromatincomprises the lexA binding site, and the lexA binding site is contactedwith a protein A tag during cell culture by expressing the protein A ina yeast cell of the invention during cell culture as described in theexamples.

A target chromatin contacted and bound by a tag as described above maybe isolated using an affinity handle of the tag. The term “isolated”,may be used herein to describe a purified preparation of a targetchromatin that is enriched for the target chromatin, but wherein thetarget chromatin is not necessarily in a pure form. That is, an isolatedtarget chromatin is not necessarily 100% pure, but may be about 10%,20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. An isolated targetchromatin may be enriched for the target chromatin, relative to achromatin in the lysed preparation that was not contacted by a tag ofthe invention. An isolated target chromatin may be enriched by 1, 2, 3,4, 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that is notcontacted by a tag of the invention. In some embodiments, an isolatedtarget chromatin is enriched by 2, 3, 4, or 5 fold relative to achromatin that was not contacted by a tag of the invention. In otherembodiments, an isolated target chromatin is enriched by 5, 6, 7, 8, 9,or 10 fold relative to a chromatin that was not contacted by a tag ofthe invention. In an exemplary embodiment, an isolated target chromatinis enriched 4, 5, or 6 fold relative to a chromatin that was notcontacted by a tag of the invention.

A target chromatin contacted and bound by a tag as described above maybe isolated using any affinity purification method known in the art. Inshort, a tagged target chromatin is bound to a substrate capable ofbinding the affinity handle. The substrate comprising a bound targetchromatin may then be washed to remove non-target chromatin and othercell debris, and the target chromatin may be released from substrate.Methods of affinity purification of material comprising an affinityhandle are known in the art and may include binding the affinity handleto a substrate capable of binding the affinity handle. The substrate maybe a gel matrix such as gel beads, the surface of a container, or achip. The tagged target chromatin bound to the substrate may then bepurified. Methods of purifying tagged molecules are known in the art andwill vary depending on the target molecule, the tag, and the substrate.For instance, if the tag is a protein A tag bound to a lexA binding sitein a target chromatin, the target chromatin may be bound to a magneticbead substrate comprising IgG, and purified using a magnet.

(e) Protein Extraction, Identification, and Determination of Labeling

Proteins and peptides associated with an isolated target chromatin areextracted from the isolated target chromatin. Methods of extractingproteins from chromatin are generally known in the art of proteinbiochemistry. Generally, any extraction protocol suitable for isolatingproteins and known to those of skill in the art may be used. Extractedproteins may also be further purified before protein identification. Forinstance, protein extracts may be further purified by differentialprecipitation, differential solubilization, ultracentrifugation, usingchromatographic methods such as size exclusion chromatography,hydrophobic interaction chromatography, ion exchange chromatography,affinity chromatography, metal binding, immunoaffinity chromatography,HPLC, or gel electrophoriesis such as SDS-PAGE and QPNC-PAGE. In apreferred embodiment, extracted proteins are further purified usingSDS-PAGE.

Extracted and purified intact proteins and post-translationalmodification of proteins may then be identified. Alternatively,extracted and purified intact proteins may be further digested, and theresulting peptide fragments are identified. In some embodiments, intactextracted proteins are identified. In preferred embodiments, extractedproteins are further digested, and the resulting peptide fragments areidentified. For instance, protein extracts may be fragmented byenzymatically digesting the proteins using a protease such as trypsin.In exemplary embodiments, extracted proteins are further digested asdescribed in the examples.

Methods of identifying proteins or protein fragments are known in theart and may include mass spectrometry (MS) analysis, or a combination ofmass spectrometry with a chromatographic technique. Non limitingexamples of mass spectrometer techniques may include tandem massspectrometry (MS/MS), matrix-assisted laser desorption/ionization sourcewith a time-of-flight mass analyzer (MALDI-TOF), inductively coupledplasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS),thermal ionization-mass spectrometry (TIMS), isotope ratio massspectrometry (IRMS), and spark source mass spectrometry (SSMS).Chromatographic techniques that may be used with MS may include gaschromatography, liquid chromatography, and ion mobility spectrometry. Ina preferred embodiment, proteins may be identified using tandem massspectrometry in combination with liquid chromatography (LC-MS/MS). Inanother preferred embodiment, post-translational modification ofproteins may be identified using tandem mass spectrometry in combinationwith liquid chromatography (LC-MS/MS).

As described above, proteins isolated with a chromatin of the inventionmay be labeled, unlabeled or a combination of labeled and unlabeledproteins. As described in Section I(d), if a target chromatin is taggedin a cell or an extract from a cell wherein proteins are metabolicallylabeled, proteins specifically associated with an isolated targetchromatin are metabolically labeled, whereas unlabeled proteins, orproteins comprising a combination of labeled and unlabeled proteins arenot specifically associated with the target chromatin. Alternatively, ifa target chromatin may be tagged in a cell or an extract from a cellwherein proteins are not metabolically labeled, proteins specificallyassociated with an isolated target chromatin are metabolically labeled,whereas unlabeled proteins, or proteins comprising a combination oflabeled and unlabeled proteins are not specifically associated with thetarget chromatin.

When an isolated and identified protein is a combination of labeled andunlabeled protein, the ratio of labeled to unlabeled protein may reflecta ratio at which a metabolically labeled cell sample and an unlabeledcell sample are combined to generate a combined cell sample, or lysatesderived from the two cell samples are combined to generate a combinedcell lysate. For instance, if a metabolically labeled cell sample and anunlabeled cell sample, or lysates derived from the two cell samples, arecombined at a ratio of 1:1, the ratio of labeled to unlabeled isolatedprotein may be 1:1.

However, since the ratio of labeled to unlabeled isolated proteindepends on the rate of exchange of the identified protein duringextraction and processing of a cell sample, a ratio of labeled tounlabeled isolated protein may differ from the ratio at which ametabolically labeled cell sample and an unlabeled cell sample arecombined to generate a combined cell sample, or lysates derived from thetwo cell samples are combined to generate a combined cell lysate. Forexample, if a metabolically labeled cell sample and an unlabeled cellsample, or lysates derived from the two cell samples, are combined at aratio of 1:1, a ratio of labeled to unlabeled isolated protein maydeviate from a ratio of 1:1. As such, a ratio of labeled to unlabeledisolated protein may be compared to a baseline for non-specificallyassociated proteins. For instance, a baseline for non-specificallyassociated proteins may be a ratio of labeled to unlabeled of one ormore proteins in a combined lysate, wherein the one or more proteins arenot associated with a chromatin. Non-limiting examples of proteins notassociated with a chromatin may include enzymes required for metabolism,receptors, and ribosomoal proteins. In preferred embodiments, proteinsnot associated with a chromatin are ribosomal proteins, and a baselinefor non-specifically associated proteins is a ratio of a labeled tounlabeled ribosomal protein, or an average of ratios of labeled tounlabeled ribosomal proteins. In a preferred embodiment, proteins notassociated with a chromatin are 20 ribosomal proteins, and a baselinefor non-specifically associated proteins is an average of ratios of the20 labeled to unlabeled ribosomal proteins.

Isolated proteins with a ratio of labeled to unlabeled isolated proteinmay be specifically associated with a chromatin if the ratio of labeledto unlabeled isolated protein is significantly different from a baselineratio. A significantly different ratio may be a ratio of labeled tounlabeled isolated protein greater than about 1, 2, 3, 4, 5, or morestandard deviations than a baseline ratio. In some embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, ormore standard deviations than a baseline ratio. In other embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1, 1.5, 2, or about 2.5 standarddeviations than a baseline ratio. In preferred embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6,1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9 or about 3standard deviations than a baseline ratio. In exemplary embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1,2.2, 2.3, 2.4, or about 2.5 standard deviations than a baseline ratio.

Methods of determining if a protein or a protein fragment is labeled canand will vary depending on the type of label. For instance, if a proteinis labeled using a tag, labeling may be determined using methodsdesigned to detect the tag. For example, determining if a proteincomprising a his-tag is tagged, untagged, or a combination of tagged anduntagged may be by detecting the proteins comprising the his tag. If aprotein is labeled using a radioactive isotope, labeling may bedetermined by determining the degree of radioactivity of isolatedproteins or protein fragments. Alternatively, if a protein is labeledusing a heavy isotope, MS analysis may be used to determine if a proteinor a protein fragment is labeled or unlabeled. Advantageously, when aprotein is labeled using a heavy isotope, MS analysis may be used toidentify a protein or a protein fragment as described above, and toderive the MS data to determine if a protein or a protein fragment islabeled, unlabeled, or a combination of labeled and unlabeled protein orprotein fragment.

In preferred embodiments, a protein is labeled using a heavy isotope,and MS analysis is used to identify a protein or a protein fragment, andto determine if a protein or a protein fragment is labeled, unlabeled,or a combination of labeled and unlabeled protein or protein fragment.Methods of deriving MS data to determine if a protein or a proteinfragment is labeled, unlabeled, or a combination of labeled andunlabeled protein or protein fragment are known in the art, and mayinclude using known computational techniques to distill MS data such asMascot Distiller, Rosetta Elucidator, and MaxQuant. In some embodiments,MS data is derived using Rosetta Elucidator. In other embodiments, MSdata is derived using MaxQuant. In preferred embodiments, MS data isderived using Mascot Distiller.

II. Method of TAL-ChAP-MS

In another aspect, the invention provides a method of isolating andidentifying proteins specifically associated with a target chromatinusing the TAL protein as described in Example 4 and FIG. 7. TheTAL-ChAP-MS approach achieves high resolution and specificity by usingthe genomic targeting ability of the TALEN system for local epiproteomeisolation and analysis. To alleviate genomic engineering for affinityenrichment of chromatin sections, a specific TAL-protein is designedwith specificity for a target chromatin. This second-generationtechnology provides quantitative identification of specifically boundproteins and histone PTMs to a native chromatin region using label-freequantitative mass spectrometry.

To determine which of the identified proteins and posttranslationalmodifications of proteins associated with a target chromatin isolatedfrom a cell are specifically or non-specifically associated with thetarget chromatin, a method of high-resolution mass spectrometry coupledwith label-free proteomics was used. One with skill in the art willappreciate that label-free quantitative proteomics methods include thefollowing fundamental steps: (i) sample preparation including proteinextraction, reduction, alkylation, and digestion; (ii) sample separationby liquid chromatography (LC or LC/LC) and analysis by MS/MS; (iii) dataanalysis including peptide/protein identification, quantification, andstatistical analysis. A method of the invention provides two cellsamples, or lysates derived from two cell samples, comprising the targetchromatin, wherein the target chromatin in one cell sample, but not bothof the cell samples is tagged. With label-free quantitative methods,each sample is separately prepared, then subjected to individualLC-MS/MS or LC/LC-MS/MS runs. As reviewed in Zhu et al., J BiomedBiotechnol 2010, and incorporated by reference herein, proteinquantification is generally based on two categories of measurements. Inthe first are the measurements of ion intensity changes such as peptidepeak areas or peak heights in chromatography. The second is based onspectral counting of identified proteins after MS/MS analysis. Peptidepeak intensity or spectral count is measured for individual LC-MS/MS orLC/LC-MS/MS runs and changes in protein abundance are calculated via adirect comparison between different analyses.

In the present invention, the method of spectral counting is used tocategorize whether proteins enriched with a section of chromatin arespecific or contaminant. As such, determining the abundance of anidentified protein in a tagged chromatin sample compared to the sameprotein in an untagged chromatin sample, may determine if the proteinwas specifically associated with the target chromatin of the invention.If a protein associated with a target chromatin is enriched in a taggedchromatin sample compared to the same protein in an untagged chromatinsample, then the protein is specifically associated with the targetchromatin. If an identified protein is not enriched in a taggedchromatin sample compared to an untagged chromatin sample, thenassociation of that protein with the target chromatin is not specific.

In the present invention, to measure enrichment of a protein, thenormalized spectral abundance factor (NSAF) is calculated for eachprotein in each lane of an SDS-PAGE gel by dividing the number ofspectral counts (normalized for the size of the protein) of a givenprotein by the sum of all normalized spectral counts of all proteins inthe gel lane. The enrichment level for each protein is identified bycalculating the fold enrichment (tagged chromatin/untagged chromatin)using the NSAF values.

(a) Cells

A target nucleic acid sequence may be isolated from any cell comprisingthe target nucleic acid sequence of the invention. A cell may be anarchaebacterium, a eubacterium, or a eukaryotic cell. For instance, acell of the invention may be a methanogen, a halophile or athermoacidophile archaeabacterium, a gram positive, a gram negative, acyanobacterium, a spirochaete, or a firmicute bacterium, a fungal cell,a moss cell, a plant cell, an animal cell, or a protist cell.

In some embodiments, a cell of the invention is a cell from an animal. Acell from an animal cell may be a cell from an embryo, a juvenile, or anadult. Suitable animals include vertebrates such as mammals, birds,reptiles, amphibians, and fish. Examples of suitable mammals includewithout limit rodents, companion animals, livestock, and primates.Non-limiting examples of rodents include mice, rats, hamsters, gerbils,and guinea pigs. Suitable companion animals include but are not limitedto cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples oflivestock include horses, goats, sheep, swine, cattle, llamas, andalpacas. Suitable primates include but are not limited to humans,capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins,spider monkeys, squirrel monkeys, and vervet monkeys. Non-limitingexamples of birds include chickens, turkeys, ducks, and geese. In someembodiments, a cell is a cell from a human.

In some embodiments, a cell may be from a model organism commonly usedin laboratory research. For instance, a cell of the invention may be anE. coli, a Bacillus subtilis, a Caulobacter crescentus, a Mycoplasmagenitalium, an Aliivibrio fischeri, a Synechocystis, or a Pseudomonasfluorescens bacterial cell; a Chlamydomonas reinhardtii, a Dictyosteliumdiscoideum, a Tetrahymena thermophila, an Emiliania huxleyi, or aThalassiosira pseudonana protist cell; an Ashbya gossypii, anAspergillus nidulans, a Coprinus cinereus, a Cunninghamella elegans, aNeurospora crassa, a Saccharomyces cerevisiae, a Schizophyllum commune,a Schizosaccharomyces pombe, or an Ustilago maydis fungal cell; anArabidopsis thaliana, a Selaginella moellendorffii, a Brachypodiumdistachyon, a Lotus japonicus, a Lemna gibba, a Zea mays, a Medicagotruncatula, a Mimulus, a tobacco, a rice, a Populus, or a Nicotianabenthamiana plant cell, a Physcomitrella patens moss; an Amphimedonqueenslandica sponge, an Arbacia punctulata sea urchin, an Aplysia seaslug, a Branchiostoma floridae deuterostome, a Caenorhabditis elegansnematode, a Ciona intestinalis sea squirt, a Daphnia spp. crustacean, aDrosophila fruit fly, a Euprymna scolopes squid, a Hydra Cnidarian, aLoligo pealei squid, a Macrostomum lignano flatworm, a Mnemiopsisleidyicomb jelly, a Nematostella vectensis sea anemone, an Oikopleuradioica free-swimming tunicate, an Oscarella carmela sponge, a Parhyalehawaiensis crustacean, a Platynereis dumerilii marine polychaetousannelid, a Pristionchus pacificus roundworm, a Schmidtea mediterraneafreshwater planarian, a Stomatogastric ganglion of various arthropodspecies, a Strongylocentrotus purpuratus sea urchin, a Symsagittiferaroscoffensis flatworm, a Tribolium castaneum beetle, a Trichoplaxadhaerens Placozoa, a Tubifex tubifex oligochaeta, a laboratory mouse, aGuinea pig, a Chicken, a Cat, a Dog, a Hamster, a Lamprey, a Medakafish, a Rat, a Rhesus macaque, a Cotton rat, a Zebra finch, a Takifugupufferfish, an African clawed frog, or a Zebrafish. In exemplaryembodiments, a cell is a Saccharomyces cerevisiae yeast cell. Inparticularly exemplary embodiments, a cell is a Saccharomyces cerevisiaeW303a yeast cell.

A cell of the invention may be derived from a tissue or from a cell linegrown in tissue culture. A cell line may be adherent or non-adherent, ora cell line may be grown under conditions that encourage adherent,non-adherent or organotypic growth using standard techniques known toindividuals skilled in the art. Cell lines and methods of culturing celllines are known in the art. Non-limiting examples of cell lines commonlycultured in a laboratory may include HeLa, a cell line from the NationalCancer Institute's 60 cancer cell lines, DU145 (prostate cancer), Lncap(prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer),PC3 (prostate cancer), T47D (breast cancer), THP-1 (acute myeloidleukemia), U87 (glioblastoma), SHSY5Y Human neuroblastoma cells, Saos-2cells (bone cancer), Vero, GH3 (pituitary tumor), PC12(pheochromocytoma), MC3T3 (embryonic calvarium), Tobacco BY-2 cells,Zebrafish ZF4 and AB9 cells, Madin-Darby canine kidney (MDCK), orXenopus A6 kidney epithelial cells.

A cell of the invention may be derived from a biological sample. As usedherein, the term “biological sample” refers to a sample obtained from asubject. Any biological sample containing a cell is suitable. Numeroustypes of biological samples are known in the art. Suitable biologicalsample may include, but are not limited to, tissue samples or bodilyfluids. In some embodiments, the biological sample is a tissue samplesuch as a tissue biopsy. The tissue biopsy may be a biopsy of a known orsuspected tumor. The biopsied tissue may be fixed, embedded in paraffinor plastic, and sectioned, or the biopsied tissue may be frozen andcryosectioned. Alternatively, the biopsied tissue may be processed intoindividual cells or an explant, or processed into a homogenate, a cellextract, a membranous fraction, or a protein extract. The sample mayalso be primary and/or transformed cell cultures derived from tissuefrom the subject. In other embodiments, the sample may be a bodilyfluid. Non-limiting examples of suitable bodily fluids include blood,plasma, serum, and urine. The fluid may be used “as is”, the cellularcomponents may be isolated from the fluid, or a protein fraction may beisolated from the fluid using standard techniques.

Suitable subjects include, but are not limited to, a human, a livestockanimal, a companion animal, a lab animal, and a zoological animal. Inone embodiment, the subject may be a rodent, e.g. a mouse, a rat, aguinea pig, etc. In another embodiment, the subject may be a livestockanimal. Non-limiting examples of suitable livestock animals may includepigs, cows, horses, goats, sheep, llamas and alpacas. In yet anotherembodiment, the subject may be a companion animal. Non-limiting examplesof companion animals may include pets such as dogs, cats, rabbits, andbirds. In yet another embodiment, the subject may be a zoologicalanimal. As used herein, a “zoological animal” refers to an animal thatmay be found in a zoo. Such animals may include non-human primates,large cats, wolves, and bears. In preferred embodiments, the animal is alaboratory animal. Non-limiting examples of a laboratory animal mayinclude rodents, canines, felines, and non-human primates. In apreferred embodiment, the subject is human.

As will be appreciated by a skilled artisan, the method of collecting abiological sample can and will vary depending upon the nature of thebiological sample and the type of analysis to be performed. Any of avariety of methods generally known in the art may be utilized to collecta biological sample. Generally speaking, the method preferably maintainsthe integrity of the sample such that chromatin can be accuratelydetected and measured according to the invention.

As described in Section II above, two cell samples, or lysates derivedfrom two cell samples may be subjected to mass-spectrometry coupled withlabel-free proteomics, one sample of which contains a tagged targetchromatin of the invention. Typically, cells in two cell samples of theinvention are from the same type of cells or they may be derived fromthe same type of cells or derived from the same biological sample. Insome embodiments, cells may comprise a heterologous protein expressed ina cell of the invention. The heterologous protein expressed in a cellmay be used for tagging a target chromatin as described in SectionII(d). In some embodiments, cells in two cell samples of the inventionare from the same type of cells. In other embodiments, cells in thefirst cell sample are derived from the same cell type as cells in thesecond cell sample.

Two cell samples of the invention may be from the same genus, species,variety or strain of cells or from the same biological sample. In aspecific embodiment, two cell samples of the invention are Saccharomycescerevisiae yeast cells or derivatives of Saccharomyces cerevisiae yeastcells. In exemplary embodiments, two cell samples of the invention areSaccharomyces cerevisiae W303a yeast cells or derivatives ofSaccharomyces cerevisiae W303a yeast cells. In exemplary embodiments,two cell samples of the invention are derivatives of Saccharomycescerevisiae W303a yeast cells, wherein-protein A tagged transcriptionactivator-like (TAL) protein engineered to bind upstream of the GAL1transcription start site is expressed in one of the cell samples ofderived Saccharomyces cerevisiae W303a yeast cells.

The number of cells in a cell sample can and will vary depending on thetype of cells, the abundance of a target chromatin in a cell, and themethod of protein identification used, among other variables. Forinstance, if a cell of the invention is Saccharomyces cerevisiae, about5×10¹⁰ to about 5×10¹², more preferably, about 1×10¹¹ to about 1×10¹²cells may be used in a cell sample. In some embodiments, about about1×10¹¹ to about 1×10¹² Saccharomyces cerevisiae cells are used in a cellsample.

Two cell samples of the invention are typically grown identically.Identically grown cell samples minimizes potential structural orfunctional differences at a target chromatin present in both cellsamples. As used herein, “grown identically” refers to cultured cellsamples grown using similar culture condition, or cells from a tissueharvested using identical harvesting techniques, or biological samplescollected, and optionally processed, via identical techniques.

(b) Chromatin

A method of the invention comprises identification of a protein andpost-translational modification of a protein associated with a targetchromatin. Generally, chromatin refers to the combination of nucleicacids and proteins in the nucleus of a eukaryotic cell. However, it iscontemplated that the term “chromatin” may also refer to the combinationof any nucleic acid sequence and proteins associated with the nucleicacid sequence in any cell.

Chromatin of the invention may be as described in Section I(b) above.

(c) Preparation of Cell Lysate

A target chromatin is isolated from a cell lysate derived from a cellsample, wherein a target chromatin is tagged in the cell sample. Themethod of isolating a target chromatin is also performed on a celllysate derived from a cell sample, wherein a target chromatin isuntagged in the cell sample. A skilled practitioner of the art willappreciate that structural and functional features of a target chromatinmust be preserved during cell lysis and isolation of the targetchromatin. The association of proteins with a target chromatin may bepreserved during cell lysis and isolation of the target chromatin usingmethods known in the art for preserving a complex of proteins with anucleic acid sequence. For instance, lysing of a cell and isolation of atarget chromatin may be performed under refrigeration or using cryogenicmethods and buffer conditions capable of preserving association ofproteins and nucleic acid sequences. In addition, a complex of proteinswith a nucleic acid may be preserved by crosslinking protein and nucleicacid complexes in a cell prior to lysing and isolating a chromatin.Crosslinking protein and nucleic acid complexes in a cell may alsocapture, or preserve, transient protein-protein and protein-nucleic acidinteractions.

In some embodiments, a complex of proteins with a nucleic acid may bepreserved by crosslinking protein and nucleic acid complexes in achromatin prior to lysing a cell and isolating the chromatin.Crosslinking is the process of joining two or more molecules such as twoproteins or a protein and a nucleic acid molecule, by a covalent bond.Molecules may be crosslinked by irradiation with ultraviolet light, orby using chemical crosslinking reagents. Chemical crosslinking reagentscapable of crosslinking proteins and nucleic acids are known in the artand may include crosslinking reagents that target amines, sulfhydryls,carboxyls, carbonyls or hydroxyls; omobifunctional or heterobifunctionalcrosslinking reagent, variable spacer arm length or zero-lengthcrosslinking reagents, cleavable or non-cleavable crosslinking reagents,and photoreactive crosslinking reagents. Non-limiting examples ofcrosslinking reagents that may be used to crosslink protein complexesand/or protein complexes and nucleic acids may include formaldehyde,glutaraldehyde, disuccinimidyl glutarate, disuccinimidyl suberate, aphotoreactive amino acid such as photo-leucine or photo-methionine, andsuccinimidyl-diazirine. The degree of crosslinking can and will varydepending on the application of a method of the invention, and may beexperimentally determined.

In a preferred embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehyde.In an exemplary embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehydeas described in the examples.

A skilled practitioner of the art will appreciate that protocols forlysing a cell can and will vary depending on the type of cell, thetarget chromatin of the invention, and the specific application of amethod of the invention. Non limiting examples of methods that may beused to lyse a cell of the invention may include cell lysis using adetergent, an enzyme such as lysozyme, incubation in a hypotonic bufferwhich causes a cell to swell and burst, mechanical disruption such asliquid homogenization by forcing a cell through a narrow space,sonication, freeze/thaw, mortar and pestle, glass beads, andcombinations thereof. In some embodiments, when a cell of the inventionis a yeast cell, the cell may be cryogenically lysed under liquidnitrogen temperature with glass beads. In exemplary embodiments, when acell of the invention is a yeast cell, the cell may be cryogenicallylysed under liquid nitrogen temperature with glass beads as described inthe examples.

Buffer conditions used during lysing and isolation of a chromatin of theinvention can and will be altered to control stringent conditions duringcell lysis and isolation to preserve association of proteins and nucleicacid sequences of a chromatin. “Stringent conditions” in the context ofchromatin isolation are conditions capable of preserving specificassociation of proteins and nucleic acids of a chromatin, but minimizingnon-specific association of proteins and nucleic acids. Stringentconditions can and will vary depending on the application of a method ofthe invention, the target chromatin of the invention, the nucleic acidsequence in a target chromatin, the proteins or protein complexesassociated with a target chromatin of the invention, whether or notproteins, protein complexes and nucleic acid sequences are crosslinked,and the conditions used for crosslinking proteins, protein complexes andnucleic acid sequences of a target chromatin. For instance, morestringent buffer conditions may be used in a method of the inventionwherein proteins, protein-protein complexes, and protein-nucleic acidcomplexes are crosslinked compared to a method of the invention whereinproteins, protein-protein complexes, and protein-nucleic acid complexesare not crosslinked. As such, stringent buffer conditions used duringcell lysis and isolation of a nucleic acid sequence of the invention maybe experimentally determined for each application wherein a method ofthe invention is used. Buffer conditions that may alter stringentconditions during cell lysis and isolation may include pH and saltconcentration. In preferred embodiments, proteins, protein-proteincomplexes, and protein-nucleic acid complexes of a target chromatin ofthe invention are crosslinked, and stringent buffer conditions are usedduring lysis and isolation of a chromatin of the invention. In exemplaryembodiments, proteins, protein-protein complexes, and protein-nucleicacid complexes of a target chromatin of the invention are crosslinked,and stringent buffer conditions are used during lysis and isolation of achromatin of the invention and are as described in the examples.

(d) Chromatin Isolation

According to the invention, the method of isolating a target chromatinis performed on cell lysates derived from cell samples, wherein onesample comprises a target chromatin that is tagged in the cell sampleand one sample comprises a target chromatin that is untagged in the cellsample. As described in Sections II(a) and II(c) above, a cell lysatecomprises a lysate of a cell sample, wherein a target chromatin istagged in one of the lysates, or one of the cell samples. A cell lysatealso comprises a lysate of a cell sample, wherein a target chromatin isnot tagged in one of the lysates, or one of the cell samples.

A target chromatin may be isolated from a mixture of chromatins orchromatin fragments in a cell lysate as described in this section. Asused herein, a target nucleic acid sequence is said to be “isolated” or“purified” when it is substantially free of proteins not associated withthe target chromatin, nucleic acid sequences other than the nucleic acidsequences associated with the target chromatin, and other cell debrisand cell contents resulting from extraction and preparation of thetarget chromatin from a cell. A target chromatin of the presentinvention may be purified to homogeneity or other degrees of purity. Ingeneral, the level of purity of an isolated target chromatin can andwill vary depending on the cell type, the specific chromatin to beisolated, and the intended use of a target chromatin of the invention.The level of purity of an isolated target chromatin may be determinedusing methods known in the art. For instance, the level of purity of anisolated target chromatin may be determined by determining the level ofpurity of a nucleic acid sequence associated with a target chromatin, bydetermining the level of purity of a protein associated with a targetchromatin, or by determining the level of enrichment of a targetchromatin, compared to a non-target chromatin in a cell. In preferredembodiments, the level of purity of an isolated target chromatin isdetermined by determining the level of enrichment of a target chromatin,compared to a non-target chromatin in a cell. Determining the level ofenrichment of a target chromatin, compared to a non-target chromatin ina cell may be as described in this section below.

A target chromatin of the invention may be isolated using methods knownin the art, such as electrophoresis, molecular, immunological andchromatographic techniques, ion exchange, hydrophobic, affinity, andreverse-phase HPLC chromatography, size exclusion chromatography,precipitation, dialysis, chromatofocusing, ultrafiltration anddiafiltration techniques, and combinations thereof. For general guidancein suitable purification techniques, see Scopes, R., ProteinPurification, Springer-Vertag, NY (1982).

In general, a method of the invention comprises isolating a targetchromatin by affinity purification, or affinity purification incombination with other methods of isolating chromatin described above.In a preferred embodiment, a method of the invention comprises isolatinga target chromatin by affinity purification. Non-limiting examples ofaffinity purification techniques that may be used to isolate a targetchromatin of the invention may include affinity chromatography,immunoaffinity chromatography, size exclusion chromatography, andcombinations thereof. See, for example, Roe (ed), Protein PurificationTechniques: A Practical Approach, Oxford University Press, 2nd edition,2001.

In essence, affinity purification of a target chromatin may comprisetagging a target chromatin by contacting the target chromatin of theinvention with a tag capable of specifically recognizing and binding oneor more portions of a target chromatin. As described in Section II, atarget chromatin from one cell sample, or lysate derived from the cellsample of the invention, but not both of the cell samples, is tagged.

A tag may be capable of specifically recognizing and binding 1, 2, 3, 4,5, 6, 7, 8, 9, or 10 components of a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and bindingone component of a target chromatin.

A tag may be capable of specifically recognizing and binding a componentin a target chromatin. A component in a target chromatin may be anucleic acid sequence in a nucleic acid associated with a targetchromatin, a protein associated with a target chromatin, or a chromatinstructural or functional feature in a target chromatin. In someembodiments, a tag is capable of specifically recognizing and binding aprotein associated with a target chromatin. In other embodiments, a tagis capable of specifically recognizing and binding a chromatinstructural or functional feature in a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and binding anucleic acid sequence associated with a target chromatin.

A nucleic acid sequence associated with a target chromatin that may bespecifically recognized and bound by a tag of the invention may be anucleic acid sequence normally found in a chromatin of a cell of theinvention. Individuals of ordinary skill in the art will recognize thata tag introduced into a cell to facilitate tagging a target chromatin ofthe invention cannot and will not disrupt a target chromatin, or astructural or functional feature of a target chromatin. Methods ofdesigning a tag capable of binding the chromatin component that do notdisrupt a chromatin of the invention may depend on the particularapplication of a method of the invention, and may be determinedexperimentally. For instance, if an application of a method of theinvention comprises promoter function, a tag may be designed to bindanywhere adjacent to the promoter, but without disrupting the promoter.

In some embodiments, a tag of the invention is a nucleic acid tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin isintroduced into a cell of the invention. In some embodiments, a tag ofthe invention is a nucleic acid tag capable of binding a nucleic acidsequence component of a chromatin, wherein the nucleic acid sequencecomponent of the chromatin is normally present in a cell of theinvention. Non-limiting examples of nucleic acid tags capable of bindinga nucleic acid sequence component of a chromatin include antisense RNAor DNA nucleic acid tags, and tags comprising modified nucleic acids andnucleic acid mimics such as peptide nucleic acids, locked nucleic acids,phosphorodiamidate morpholino oligomers (PMO). In some embodiments, atag of the invention is a nucleic acid tag comprising lockednucleotides. For instance, a nucleic acid tag comprising lockednucleotides may be as described in US20110262908 or US20120040857, and apeptide nucleic acid tag may be as described in Boffa et al. 1995 PNAS92:1901-1905, the disclosures of all of which are incorporated herein intheir entirety.

In specific embodiments, a tag of the invention is a protein tag capableof binding a nucleic acid sequence component of a chromatin, wherein thenucleic acid sequence component of the chromatin is a nucleic acidsequence normally found in a chromatin of a cell of the invention. Nonlimiting examples of a protein tag capable of binding a nucleic acidsequence normally found in a chromatin of a cell may be a nucleic acidbinding protein such as protein A, the Lac repressor, a zinc fingerprotein, a transcription activator protein capable of binding a nucleicacid, or a transcription activator-like (TAL) protein. In oneembodiment, a tag of the invention is a transcription activator proteincapable of binding a nucleic acid sequence normally found in a chromatinof a cell of the invention. In another embodiment, a tag of theinvention is a zinc finger protein capable of binding a nucleic acidsequence normally found in a chromatin of a cell of the invention. In anexemplary embodiment, a tag of the invention is transcriptionactivator-like (TAL) protein capable of binding a nucleic acid sequencenormally found in a chromatin of a cell of the invention.

A nucleic acid binding protein tag of the invention may be a wild typenucleic acid binding protein capable of binding a nucleic acid sequencenormally found in a target chromatin. Alternatively, a nucleic acidbinding protein tag of the invention may be engineered to specificallyrecognize a nucleic acid sequence component normally found in a targetchromatin of the invention. Individuals of ordinary skill in the artwill recognize that nucleic acid binding proteins such as zinc fingerproteins, transcription activator proteins, and transcriptionactivator-like (TAL) proteins may be engineered to have novel nucleicacid binding specificity compared to naturally-occurring forms of theproteins. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, andU.S. Pate. Appl. Nos 20110239315, 20120110685, and 20120270273, thedisclosures of which are incorporated by reference herein in theirentireties. In some embodiments, a nucleic acid binding protein tag ofthe invention is a wild type nucleic acid binding protein capable ofbinding a nucleic acid sequence normally found in a target chromatin. Inother embodiments, a nucleic acid binding protein tag of the inventionis a nucleic acid binding protein engineered to specifically recognize anucleic acid sequence component of a target chromatin of the invention.In a preferred embodiment, a nucleic acid binding protein tag of theinvention is a zinc finger protein engineered to specifically recognizea nucleic acid sequence component of a target chromatin of theinvention. In an exemplary embodiment, a nucleic acid binding proteintag of the invention is a TAL protein engineered to specificallyrecognize a nucleic acid sequence component of a target chromatin of theinvention.

A tag of the invention may further comprise one or more affinityhandles. As used herein, the term “affinity handle” may refer to anyhandle that may be bound by a substrate for affinity purification, asdescribed below. A tag may comprise one or more than one affinityhandle. The inclusion of more than one affinity handle in a tag of theinvention may significantly increase the efficiency of affinitypurification for a low copy number chromatin target. As such, a tag mayfurther comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more affinity handles.In a preferred embodiment, a tag of the invention comprises one affinityhandle.

Affinity handles may include any affinity handle for which a cognatebinding agent is readily available. An affinity handle may be anaptamer, an antibody, an antibody fragment, a double-stranded DNAsequence, modified nucleic acids and nucleic acid mimics such as peptidenucleic acids, locked nucleic acids, phosphorodiamidate morpholinooligomers (PMO), a ligand, a ligand fragment, a receptor, a receptorfragment, a polypeptide, a peptide, a coenzyme, a coregulator, anallosteric molecule, non-immunoglobulin scaffolds such as Affibodies,Anticalins, designed Ankyrin repeat proteins and others, an ion, or asmall molecule for which a cognate binding agent is readily available.The term “aptamer” refers to a polypeptide or a polynucleotide capableof binding to a target molecule at a specific region. It is generallyaccepted that an aptamer, which is specific in its binding to anypolypeptide, may be synthesized and/or identified by in vitro evolutionmethods. Non limiting examples of handles that may be suitable forisolating a chromatin may include biotin or a biotin analogue such asdesthiobiotin, digoxigenin, dinitrophenol or fluorescein, antigenicpolypeptides such as protein A, or peptide ‘tags’ such as polyhistidine,FLAG, HA and Myc tags. In preferred embodiments, a tag of the inventioncomprises an antigenic polypeptide as an affinity handle. In otherpreferred embodiments, a tag of the invention comprises protein A orderivatives thereof as an affinity handle. In a specific embodiment, atag of the invention comprises protein A-tagged TAL protein. The TALprotein can be engineered to specifically recognize a nucleic acidsequence component of a target chromatin of the invention. As such, TALmay be used as an affinity purification tag for purifying a targetchromatin. Protein A comprises an affinity handle capable of bindingIgG. In exemplary embodiments, a tag of the invention comprises theprotein A tagged TAL protein engineered to bind upstream of the GAL1transcription start site.

A target chromatin may be contacted with a tag at any time during amethod of the invention leading to isolation of target chromatin. Forinstance, a target chromatin may be contacted with a protein tag duringcell culture by expressing the protein tag in a cell of the invention.Alternatively, a target chromatin may be contacted with a tag after cellculture but before cell lysis, after cell lysis, or after fragmentationof chromatin to generate chromatin fragments comprising a targetchromatin. In such embodiments, a tag may be added to the cell cultureor cell lysate as a recombinant protein. The recombinant protein may beexpressed, isolated and purified via methods standard in the art forprotein purification.

In some embodiments, a target chromatin is contacted with a tag aftercell culture but before cell lysis. As such, a tag may be introducedinto a cell before cell lysis. Methods of introducing a tag into a cellof the invention can and will vary depending on the type of cell, thetag, and the application of a method of the invention. For instance, anucleic acid tag may be electroporated into a cell after culture. Inother embodiments, a target chromatin is contacted with a tag after celllysis. In such an embodiment, a tag may be added to the cell lysate as arecombinant protein. In yet other embodiments, a target chromatin iscontacted with a tag after cell lysis and chromatin fragmentation. Incertain embodiments, a target chromatin is contacted with a tag duringcell culture by expressing the tag in a cell of the invention duringcell culture. In exemplary embodiments, a target chromatin is contactedwith a protein A tagged TAL protein during cell culture by expressingthe protein A tagged TAL protein in a cell of the invention during cellculture.

A target chromatin contacted and bound by a tag as described above maybe isolated using an affinity handle of the tag. The term “isolated”,may be used herein to describe a purified preparation of a targetchromatin that is enriched for the target chromatin, but wherein thetarget chromatin is not necessarily in a pure form. That is, an isolatedtarget chromatin is not necessarily 100% pure, but may be about 10%,20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. An isolated targetchromatin may be enriched for the target chromatin, relative to achromatin in the lysed preparation that was not contacted by a tag ofthe invention. An isolated target chromatin may be enriched by 1, 2, 3,4, 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that is notcontacted by a tag of the invention. In some embodiments, an isolatedtarget chromatin is enriched by 2, 3, 4, or 5 fold relative to achromatin that was not contacted by a tag of the invention. In otherembodiments, an isolated target chromatin is enriched by 5, 6, 7, 8, 9,or 10 fold relative to a chromatin that was not contacted by a tag ofthe invention. In an exemplary embodiment, an isolated target chromatinis enriched 4, 5, or 6 fold relative to a chromatin that was notcontacted by a tag of the invention.

A target chromatin contacted and bound by a tag as described above maybe isolated using any affinity purification method known in the art. Inshort, a tagged target chromatin is bound to a substrate capable ofbinding the affinity handle. The substrate comprising a bound targetchromatin may then be washed to remove non-target chromatin and othercell debris, and the target chromatin may be released from substrate.Methods of affinity purification of material comprising an affinityhandle are known in the art and may include binding the affinity handleto a substrate capable of binding the affinity handle. The substrate maybe a gel matrix such as gel beads, the surface of a container, or achip. The tagged target chromatin bound to the substrate may then bepurified. Methods of purifying tagged molecules are known in the art andwill vary depending on the target molecule, the tag, and the substrate.For instance, if the tag is a TAL-protein A tag bound to a site in atarget chromatin, the target chromatin may be bound to a magnetic beadsubstrate comprising IgG, and purified using a magnet.

(e) Protein Extraction, Identification, and Determination of Labeling

Proteins and peptides associated with an isolated target chromatin areextracted from the isolated target chromatin. Methods of extractingproteins from chromatin are generally known in the art of proteinbiochemistry. Generally, any extraction protocol suitable for isolatingproteins and known to those of skill in the art may be used. Extractedproteins may also be further purified before protein identification. Forinstance, protein extracts may be further purified by differentialprecipitation, differential solubilization, ultracentrifugation, usingchromatographic methods such as size exclusion chromatography,hydrophobic interaction chromatography, ion exchange chromatography,affinity chromatography, metal binding, immunoaffinity chromatography,HPLC, or gel electrophoriesis such as SDS-PAGE and QPNC-PAGE. In apreferred embodiment, extracted proteins are further purified usingSDS-PAGE.

Extracted and purified intact proteins and post-translationalmodification of proteins may then be identified. Alternatively,extracted and purified intact proteins may be further digested, and theresulting peptide fragments are identified. In some embodiments, intactextracted proteins are identified. In preferred embodiments, extractedproteins are further digested, and the resulting peptide fragments areidentified. For instance, protein extracts may be fragmented byenzymatically digesting the proteins using a protease such as trypsin.In exemplary embodiments, extracted proteins are further digested asdescribed in the examples.

Methods of identifying proteins or protein fragments are known in theart and may include mass spectrometry (MS) analysis, or a combination ofmass spectrometry with a chromatographic technique. Non limitingexamples of mass spectrometer techniques may include tandem massspectrometry (MS/MS), matrix-assisted laser desorption/ionization sourcewith a time-of-flight mass analyzer (MALDI-TOF), inductively coupledplasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS),thermal ionization-mass spectrometry (TIMS), isotope ratio massspectrometry (IRMS), and spark source mass spectrometry (SSMS).Chromatographic techniques that may be used with MS may include gaschromatography, liquid chromatography, and ion mobility spectrometry. Ina preferred embodiment, proteins may be identified using tandem massspectrometry in combination with liquid chromatography (LC-MS/MS). Inanother preferred embodiment, post-translational modification ofproteins may be identified using tandem mass spectrometry in combinationwith liquid chromatography (LC-MS/MS).

In the present invention, the method of label-free proteomics is used tocategorize whether proteins enriched with a section of chromatin arespecific or contaminant. Label-free methods of quantifying proteins orprotein fragments are known in the art. In label-free quantitativeproteomics, each sample is separately prepared, then subjected toindividual methods of identifying proteins or protein fragments whichmay include LC-MS/MS or LC/LC-MS/MS. According to the invention, onesample comprises a target chromatin that is tagged in the cell sampleand one sample comprises a target chromatin that is untagged in the cellsample. Label-free protein quantification is generally based on twocategories of measurement. In the first are the measurements of ionintensity changes such as peptide peak areas or peak heights inchromatography. The second is based on the spectral counting ofidentified proteins after MS/MS analysis. Peptide peak intensity orspectral count is measured for individual LC-MS/MS or LC/LC-MS/MS runsand changes in protein abundance are calculated via a direct comparisonbetween different analyses. In a preferred embodiment, the proteinsidentified using mass spectrometry are quantified and identified asenriched in the sample containing the tagged target chromatin comparedto the sample containing the untagged target chromatin using label-freeproteomics. In an exemplary embodiment, the proteins identified usingmass spectrometry are quantified and identified as enriched in thesample containing the tagged target chromatin compared to the samplecontaining the untagged target chromatin using spectral counting.

The method of protein quantification by spectral count is known in theart and is reviewed in Zhu et al., J Biomed Biotechnol 2010, which isincorporated by reference herein. In spectral counting, relative proteinquantification is achieved by comparing the number of identified MS/MSspectra from a protein of one sample to the same protein in the othersample. In the present invention, one sample comprises a targetchromatin that is tagged and another sample comprises a target chromatinthat is untagged. Protein quantification in spectral counting utilizesthe fact that an increase in protein abundance typically results in anincrease in the number of its proteolytic peptides, and vice versa. Thisincreased number of (tryptic) digests then usually results in anincrease in protein sequence coverage, the number of identified uniquepeptides, and the number of identified total MS/MS spectra (spectralcount) for each protein.

As such, determining the abundance of an identified protein in a taggedchromatin sample compared to the same protein in an untagged chromatinsample, may determine if the protein was specifically associated with atarget chromatin of the invention. If an identified protein associatedwith a target chromatin is in enriched in a tagged chromatin samplecompared to the same protein in an untagged chromatin sample, then theprotein was specifically associated with a target chromatin of theinvention. If an identified protein is not enriched in a taggedchromatin sample compared to an untagged chromatin sample, then theprotein is non-specifically associated with a target chromatin of theinvention.

A skilled artisan in spectral counting will appreciate thatnormalization and statistical analysis of spectral counting datasets arenecessary for accurate and reliable detection of protein changes. Sincelarge proteins tend to contribute more peptide/spectra than small ones,a normalized spectral abundance factor (NSAF) is defined to account forthe effect of protein length on spectral count. NSAF is calculated asthe number of spectral counts (SpC) identifying a protein, divided bythe protein's length (L), divided by the sum of SpC/L for all proteinsin the experiment. NSAF allows the comparison of abundance of individualproteins in multiple independent samples and has been applied toquantify the expression changes in various complexes.

In the present invention, to measure enrichment of a protein, thenormalized spectral abundance factor (NSAF) is calculated for eachprotein in each lane of an SDS-PAGE gel by dividing the number ofspectral counts (normalized for the size of the protein) of a givenprotein by the sum of all normalized spectral counts of all proteins inthe gel lane. The enrichment level for each protein is identified bycalculating the fold enrichment (tagged chromatin/untagged chromatin)using the NSAF values. In an exemplary embodiment, proteins enriched ina sample containing a tagged target chromatin compared to a samplecontaining an untagged target chromatin are enriched by at least about 2fold. In other embodiments, proteins enriched in a sample containing atagged target chromatin compared to a sample containing the untaggedtarget chromatin are enriched by at least about 1.5 fold. In otherembodiments, proteins enriched in a sample containing a tagged targetchromatin compared to a sample containing an untagged target chromatinare enriched by at least about 3 fold, about 4 fold, about 5 fold, about6 fold, about 7 fold, about 8 fold, about 9 fold, about 10 fold, about11 fold, about 12 fold, about 13 fold, about 14 fold, about 15 fold,about 16 fold, about 17 fold, about 18 fold, about 19 fold or about 20fold. As such, a protein enriched by at least about 2 fold in a taggedchromatin sample compared to an untagged chromatin sample, isspecifically associated with the chromatin. For instance, a baseline fornon-specifically associated proteins may be proteins enriched by lessthan about 1.5 fold in a tagged chromatin sample compared to an untaggedchromatin sample, wherein one or more proteins are not associated withchromatin. Non-limiting examples of proteins not associated with achromatin may include enzymes required for metabolism, receptors, andribosomal proteins. In preferred embodiments, proteins not associatedwith a chromatin are ribosomal proteins, and a baseline fornon-specifically associated proteins is an enrichment less than about1.5 fold in a tagged chromatin sampled compared to an untagged chromatinsample. In an exemplary embodiment, proteins or protein fragmentsenriched by at least 15 fold in a tagged chromatin sample compared to anuntagged chromatin sample are specifically associated with a targetchromatin.

In preferred embodiments, a target chromatin is tagged in one cellsample and a target chromatin is untagged in a second cell sample, andMS analysis is used to identify proteins or protein fragments isolatedduring affinity purification of each sample, and label-free proteomicsis used to determine if a protein or a protein fragment is specificallyor non-specifically associated with the target chromatin. Methods ofderiving MS data to identify proteins or protein fragments are known inthe art, and may include using known computational techniques to distillMS data such as Mascot Distiller, Rosetta Elucidator, and MaxQuant. Insome embodiments, MS data is derived using Rosetta Elucidator. In otherembodiments, MS data is derived using MaxQuant. In preferredembodiments, MS data is derived using Mascot Distiller.

III. Method of CRISPR-ChAP-MS

In yet another aspect, the invention provides a method of isolating andidentifying proteins specifically associated with a target chromatinusing the Cas9 and guide RNA (gRNA) components of the CRISPR system asdescribed in Example 6 and FIG. 9. The CRISPR-ChAP-MS approach providesa new tool to study epigenetic regulation. Identification of proteinsand histone PTMs at 1 kb resolution does not depend on a prioriknowledge of a protein/PTM target, which distinguishes this method fromtraditional ChIP. This third-generation technology provides quantitativeidentification of specifically bound proteins and histone PTMs with anenhanced ability to isolate targeted chromatin only requiringsite-directed mutagenesis to alter the gRNA for genomic targeting.

The present disclosure provides a method of identifying proteinsincluding proteins comprising posttranslational modificationsspecifically associated with a target chromatin in a cell. The methodcomprises providing a first cell sample comprising nucleic acid bindingproteins and the target chromatin, wherein the target chromatin istagged by contacting the target chromatin with a tag capable ofspecifically recognizing and binding one or more portions of the targetchromatin and wherein the tag comprises an affinity handle, and a secondcell sample comprising nucleic acid binding proteins and the targetchromatin, wherein the target chromatin is not tagged by contacting thetarget chromatin with a non-functional tag that is not capable ofspecifically recognizing and binding one or more portions of the targetchromatin and wherein the non-functional tag comprises an affinityhandle. Affinity handle from each sample is isolated wherein affinityhandle isolated from the first cell sample consists of affinity handlebound to tagged target chromatin bound to specifically associatednucleic acid binding proteins and affinity handle bound tonon-specifically associated nucleic acid binding proteins and affinityhandle isolated from the second cell sample consists of affinity handlebound to non-specifically associated nucleic acid binding proteins,wherein isolating the affinity handle enriches for the tagged targetchromatin. Bound protein in each cell sample is identified. Then, theamount of each bound protein in each cell sample is determined, whereinbound proteins that are enriched in the first cell sample as compared tothe second cell sample are specifically associated with the taggedchromatin in the first cell sample.

The key to success with the CRISPR-ChAP-MS is the enhanced ability toisolate targeted chromatin. Further, CRISPR-ChAP-MS only requiressite-directed mutagenesis to alter the gRNA for genomic targeting, whichprovides a more cost effective approach that can easily be multiplexedto target additional sites. The chromatin enrichment methodologydescribed herein is quantitative mass spectrometry used to determineproteins/PTMs specific to the isolated chromatin. The mass spectrometricapproach used in the CRISPR-ChAP-MS approach is label-free. Withlabel-free quantitative methods, each sample is separately prepared,then subjected to individual LC-MS/MS or LC/LC-MS/MS runs. The method ofspectral counting is used to categorize whether proteins enriched with asection of chromatin are specific or contaminant. As such, determiningthe abundance of an identified protein in a tagged chromatin samplecompared to the same protein in an untagged chromatin sample, maydetermine if the protein was specifically associated with the targetchromatin of the invention. If a protein associated with a targetchromatin is enriched in a tagged chromatin sample compared to the sameprotein in an untagged chromatin sample, then the protein isspecifically associated with the target chromatin. If an identifiedprotein is not enriched in a tagged chromatin sample compared to anuntagged chromatin sample, then association of that protein with thetarget chromatin is not specific.

(a) Cells

A target nucleic acid sequence may be isolated from any cell comprisingthe target nucleic acid sequence of the invention. According to theinvention, a method comprises, in part, providing a first cell sampleand a second cell sample. A cell of a cell sample of the invention maybe an archaebacterium, a eubacterium, or a eukaryotic cell. Forinstance, a cell of a cell sample of the invention may be a methanogen,a halophile or a thermoacidophile archaeabacterium, a gram positive, agram negative, a cyanobacterium, a spirochaete, or a firmicutebacterium, a fungal cell, a moss cell, a plant cell, an animal cell, ora protist cell.

In some embodiments, a cell of a cell sample of the invention is a cellfrom an animal. A cell from an animal cell may be a cell from an embryo,a juvenile, or an adult. Suitable animals include vertebrates such asmammals, birds, reptiles, amphibians, and fish. Examples of suitablemammals include without limit rodents, companion animals, livestock, andprimates. Non-limiting examples of rodents include mice, rats, hamsters,gerbils, and guinea pigs. Suitable companion animals include but are notlimited to cats, dogs, rabbits, hedgehogs, and ferrets. Non-limitingexamples of livestock include horses, goats, sheep, swine, cattle,llamas, and alpacas. Suitable primates include but are not limited tohumans, capuchin monkeys, chimpanzees, lemurs, macaques, marmosets,tamarins, spider monkeys, squirrel monkeys, and vervet monkeys.Non-limiting examples of birds include chickens, turkeys, ducks, andgeese. In some embodiments, a cell is a cell from a human.

In some embodiments, a cell of a cell sample may be from a modelorganism commonly used in laboratory research. For instance, a cell ofthe invention may be an E. coli, a Bacillus subtilis, a Caulobactercrescentus, a Mycoplasma genitalium, an Aliivibrio fischeri, aSynechocystis, or a Pseudomonas fluorescens bacterial cell; aChlamydomonas reinhardtii, a Dictyostelium discoideum, a Tetrahymenathermophila, an Emiliania huxleyi, or a Thalassiosira pseudonana protistcell; an Ashbya gossypii, an Aspergillus nidulans, a Coprinus cinereus,a Cunninghamella elegans, a Neurospora crassa, a Saccharomycescerevisiae, a Schizophyllum commune, a Schizosaccharomyces pombe, or anUstilago maydis fungal cell; an Arabidopsis thaliana, a Selaginellamoellendorffii, a Brachypodium distachyon, a Lotus japonicus, a Lemnagibba, a Zea mays, a Medicago truncatula, a Mimulus, a tobacco, a rice,a Populus, or a Nicotiana benthamiana plant cell, a Physcomitrellapatens moss; an Amphimedon queenslandica sponge, an Arbacia punctulatasea urchin, an Aplysia sea slug, a Branchiostoma floridae deuterostome,a Caenorhabditis elegans nematode, a Ciona intestinalis sea squirt, aDaphnia spp. crustacean, a Drosophila fruit fly, a Euprymna scolopessquid, a Hydra Cnidarian, a Loligo pealei squid, a Macrostomum lignanoflatworm, a Mnemiopsis leidyicomb jelly, a Nematostella vectensis seaanemone, an Oikopleura dioica free-swimming tunicate, an Oscarellacarmela sponge, a Parhyale hawaiensis crustacean, a Platynereisdumerilii marine polychaetous annelid, a Pristionchus pacificusroundworm, a Schmidtea mediterranea freshwater planarian, aStomatogastric ganglion of various arthropod species, aStrongylocentrotus purpuratus sea urchin, a Symsagittifera roscoffensisflatworm, a Tribolium castaneum beetle, a Trichoplax adhaerens Placozoa,a Tubifex tubifex oligochaeta, a laboratory mouse, a guinea pig, achicken, a cat, a dog, a hamster, a lamprey, a medaka fish, a rat, arhesus macaque, a cotton rat, a zebra finch, a Takifugu pufferfish, anAfrican clawed frog, or a zebrafish. In exemplary embodiments, a cell isa Saccharomyces cerevisiae yeast cell. In particularly exemplaryembodiments, a cell is a Saccharomyces cerevisiae W303a yeast cell.

A cell of a cell sample of the invention may be derived from a tissue orfrom a cell line grown in tissue culture. A cell line may be adherent ornon-adherent, or a cell line may be grown under conditions thatencourage adherent, non-adherent or organotypic growth using standardtechniques known to individuals skilled in the art. Cell lines andmethods of culturing cell lines are known in the art. Non-limitingexamples of cell lines commonly cultured in a laboratory may includeHeLa, a cell line from the National Cancer Institute's 60 cancer celllines, DU145 (prostate cancer), Lncap (prostate cancer), MCF-7 (breastcancer), MDA-MB-438 (breast cancer), PC3 (prostate cancer), T47D (breastcancer), THP-1 (acute myeloid leukemia), U87 (glioblastoma), SHSY5YHuman neuroblastoma cells, Saos-2 cells (bone cancer), Vero, GH3(pituitary tumor), PC12 (pheochromocytoma), MC3T3 (embryonic calvarium),Tobacco BY-2 cells, Zebrafish ZF4 and AB9 cells, Madin-Darby caninekidney (MDCK), or Xenopus A6 kidney epithelial cells.

A cell of a cell sample may be derived from a biological sample. As usedherein, the term “biological sample” refers to a sample obtained from asubject. Any biological sample containing a cell is suitable. Numeroustypes of biological samples are known in the art. Suitable biologicalsample may include, but are not limited to, tissue samples or bodilyfluids. In some embodiments, the biological sample is a tissue samplesuch as a tissue biopsy. The tissue biopsy may be a biopsy of a known orsuspected tumor. The biopsied tissue may be fixed, embedded in paraffinor plastic, and sectioned, or the biopsied tissue may be frozen andcryosectioned. Alternatively, the biopsied tissue may be processed intoindividual cells or an explant, or processed into a homogenate, a cellextract, a membranous fraction, or a protein extract. The sample mayalso be primary and/or transformed cell cultures derived from tissuefrom the subject. In other embodiments, the sample may be a bodilyfluid. Non-limiting examples of suitable bodily fluids include blood,plasma, serum, and urine. The fluid may be used “as is”, the cellularcomponents may be isolated from the fluid, or a protein fraction may beisolated from the fluid using standard techniques.

Suitable subjects include, but are not limited to, a human, a livestockanimal, a companion animal, a lab animal, and a zoological animal. Inone embodiment, the subject may be a rodent, e.g. a mouse, a rat, aguinea pig, etc. In another embodiment, the subject may be a livestockanimal. Non-limiting examples of suitable livestock animals may includepigs, cows, horses, goats, sheep, llamas and alpacas. In yet anotherembodiment, the subject may be a companion animal. Non-limiting examplesof companion animals may include pets such as dogs, cats, rabbits, andbirds. In yet another embodiment, the subject may be a zoologicalanimal. As used herein, a “zoological animal” refers to an animal thatmay be found in a zoo. Such animals may include non-human primates,large cats, wolves, and bears. In preferred embodiments, the animal is alaboratory animal. Non-limiting examples of a laboratory animal mayinclude rodents, canines, felines, and non-human primates. In apreferred embodiment, the subject is human.

As will be appreciated by a skilled artisan, the method of collecting abiological sample can and will vary depending upon the nature of thebiological sample and the type of analysis to be performed. Any of avariety of methods generally known in the art may be utilized to collecta biological sample. Generally speaking, the method preferably maintainsthe integrity of the sample such that chromatin can be accuratelydetected and measured according to the invention.

As described in Section III above, two cell samples, or lysates derivedfrom two cell samples may be subjected to mass-spectrometry coupled withlabel-free proteomics, one sample of which contains a tagged targetchromatin of the invention. Typically, cells in a first cell sample anda second cell sample of the invention are from the same type of cells ormay be derived from the same type of cells or derived from the samebiological sample. In some embodiments, cells may comprise aheterologous nucleic acid expressed in a cell of the invention, and mayalso comprise a heterologous protein expressed in a cell of theinvention. The heterologous nucleic acid and protein expressed in a cellmay be used for tagging a chromatin of the invention as described inSection III(c). In an exemplary embodiment, cells from a first cellsample may comprise a heterologous nucleic acid and protein expressed ina cell of the invention, and cells from a second cell sample maycomprise a heterologous protein expressed in a cell of the invention.

A first cell sample and a second cell sample of the invention may befrom the same genus, species, variety or strain of cells or from thesame biological sample. In an exemplary embodiment, a first cell sampleand a second cell sample of the invention are Saccharomyces cerevisiaeyeast cells.

The number of cells in a cell sample can and will vary depending on thetype of cells, the abundance of a target chromatin in a cell, and themethod of protein identification used, among other variables. Forinstance, about 1×10⁵ to about 1×10¹² cells may be used. Accordingly,about 1×10⁵, about 1×10⁶, about 1×10⁷, about 1×10⁸, about 1×10⁹, about1×10¹⁰, about 1×10¹¹, about 1×10¹², or more cells may be used.Preferably, about 1×10⁹ to about 1×10¹¹ cells may be used in a cellsample. In some embodiments, about 1×10¹⁰ cells are used in a cellsample. In an exemplary embodiment, about 1×10¹⁰ Saccharomycescerevisiae cells are used.

A first cell sample and a second cell sample of the invention aretypically grown identically. Identically grown cell samples minimizespotential structural or functional differences at a target chromatinpresent in both cell samples. As used herein, “grown identically” refersto cultured cell samples grown using similar culture condition, or cellsfrom a tissue harvested using identical harvesting techniques, orbiological samples collected, and optionally processed, via identicaltechniques.

(b) Chromatin

According to the invention, a first cell sample and a second cell sampleof the invention comprise nucleic acid binding proteins and a targetchromatin. As used herein, “nucleic acid binding proteins” refers toproteins that bind nucleic acid. Nucleic acid binding proteins areproteins that are composed of nucleic acid-binding domains and thus havespecific or general specificity for either single or double strandednucleic acid. A nucleic acid binding protein may bind nucleic acidspecifically or nonspecifically. Non-specific association of nucleicacid binding proteins with chromatin makes it challenging to identifyproteins that are specifically bound to chromatin. The methodology ofthe present disclosure overcomes this challenge by reducing the amountof non-specific proteins bound to chromatin and enriching for proteinsspecifically bound to chromatin.

As used herein, “chromatin” refers to a target nucleic acid sequencethat may be isolated from a cell. Generally, chromatin refers to thecombination of nucleic acids and proteins in the nucleus of a eukaryoticcell. However, it is contemplated that the term “chromatin” may alsorefer to the combination of a nucleic acid sequence and proteinsassociated with the nucleic acid sequence in a cell.

A chromatin of the invention may comprise single stranded nucleic acid,double stranded nucleic acid, or a combination thereof. In someembodiments, a chromatin comprises single stranded nucleic acid. Inother embodiments, a chromatin comprises a combination of singlestranded and double stranded nucleic acids. In yet other embodiments, achromatin comprises double stranded nucleic acid.

A chromatin of the invention may comprise a ribonucleic acid (RNA), adeoxyribonucleic acid (DNA), or a combination of RNA and DNA. In someembodiments, a chromatin of the invention comprises a combination of aRNA sequence and proteins associated with the RNA sequence in a cell.Non-limiting examples of RNA sequences may include mRNA, and non-codingRNA such as tRNA, rRNA, snoRNAs, microRNAs, siRNAs, piRNAs and the longnoncoding RNA (lncRNA). In preferred embodiments, a chromatin of theinvention comprises a combination of a DNA sequence and proteinsassociated with the DNA sequence in a cell. In other preferredembodiments, a chromatin of the invention comprises a combination of RNAand DNA sequences, and proteins associated with the RNA and DNA sequencein a cell. Non limiting examples of chromatin that may comprise acombination of RNA and DNA may include genomic DNA undergoingtranscription, or genomic DNA comprising non-coding RNA such as lncRNA.

A chromatin of the invention may be genomic chromatin such as, chromatinfrom a chromosome of a cell, or chromatin from an organelle in the cell.Alternatively, a chromatin may be chromatin from an extrachromosomalnucleic acid sequence. In some embodiments, a chromatin of the inventionis chromatin from an organelle in the cell. Non-limiting examples of achromatin from an organelle may include mitochondrial nucleic acidsequence in plant and animal cells, and a chloroplast nucleic acidsequence in plant cells. In some embodiments, a nucleic acid sequence ofthe invention is a mitochondrial nucleic acid sequence. In otherembodiments, a nucleic acid sequence of the invention is a chloroplastnucleic acid sequence.

In some embodiments, a chromatin of the invention is chromatin from anextrachromosomal nucleic acid sequence. The term “extrachromosomal,” asused herein, refers to any nucleic acid sequence not contained withinthe cell's genomic nucleic acid sequence. An extrachromosomal nucleicacid sequence may comprise some sequences that are identical or similarto genomic sequences in the cell, however, an extrachromosomal nucleicacid sequence as used herein does not integrate with genomic sequencesof the cell. Non-limiting examples of an extrachromosomal nucleic acidsequence may include a plasmid, a virus, a cosmid, a phasmid, and aplasmid.

In some preferred embodiments, a chromatin of the invention is genomicchromatin. In exemplary embodiments, a chromatin of the invention isgenomic chromatin of a eukaryotic cell. A eukaryotic cell of theinvention may be as described in Section III(a) above.

Primary functions of genomic chromatin of a eukaryotic cell may be DNApackaging into a smaller volume to fit in the cell, strengthening of theDNA to allow mitosis, prevent DNA damage, and to control gene expressionand DNA replication. As described above, genomic chromatin of aeukaryotic cell may comprise DNA sequences and a plurality ofDNA-binding proteins as well as certain RNA sequences, assembled intohigher order structural or functional regions. As used herein, a“structural or functional feature of a chromatin”, refers to a chromatinfeature characterized by, or encoding, a function such as a regulatoryfunction of a promoter, terminator, translation initiation, enhancer,etc., or a structural feature such as heterochromatin, euchromatin, anucleosome, a telomere, or a centromere. A physical feature of a nucleicacid sequence may comprise a functional role and vice versa. Asdescribed below, a chromatin of the invention may be a chromatinfragment, and as such may comprise a fragment of a physical orfunctional feature of a chromatin, or no physical or functional featuresor known physical or functional features.

The primary protein components of genomic eukaryotic chromatin arehistones that compact the DNA into a nucleosome. The nucleosomecomprises an octet of histone proteins around which is wound a stretchof double stranded DNA sequence of about 150 to about 250 bp in length.Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1may act to link adjacent nucleosomes together into a higher orderstructure. Histones are subject to post translational modification whichmay affect their function in regulating chromatin function. Suchmodifications may include methylation, citrullination, acetylation,phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation.

Many further polypeptides and protein complexes interact with thenucleosome and the histones to regulate chromatin function. A“polypeptide complex” as used herein, is intended to describe proteinsand polypeptides that assemble together to form a unitary association offactors. The members of a polypeptide complex may interact with eachother via non-covalent or covalent bonds. Typically members of apolypeptide complex will cooperate to enable binding either to a nucleicacid sequence or to polypeptides and proteins already associated with orbound to a nucleic acid sequence in chromatin. Chromatin associatedpolypeptide complexes may comprise a plurality of proteins and/orpolypeptides which each serve to interact with other polypeptides thatmay be permanently associated with the complex or which may associatetransiently, dependent upon cellular conditions and position within thecell cycle. Hence, particular polypeptide complexes may vary in theirconstituent members at different stages of development, in response tovarying physiological conditions or as a factor of the cell cycle. Byway of example, in animals, polypeptide complexes with known chromatinremodelling activities include Polycomb group gene silencing complexesas well as Trithorax group gene activating complexes.

A chromatin of the invention may be an intact and complete chromatinfrom the cell, or may be a fragment of a chromatin in a cell. In someembodiments, a chromatin of the invention is an intact chromatinisolated from a cell. For instance, a chromatin of the invention may bea plasmid, a cosmid, or a phage chromatin or a complete organellarchromatin. In preferred embodiments, a chromatin of the invention is afragment of a chromatin from a cell. In exemplary embodiments, achromatin of the invention is a fragment of a genomic chromatin from acell.

When a chromatin of the invention is a fragment of a chromatin in acell, any method of fragmenting a chromatin known in the art may beused. Such methods may include physical methods of fragmenting achromatin, or enzymatic digestion of a nucleic acid sequence of achromatin. In some embodiments, a fragment of a chromatin may begenerated using enzymatic digestion of a nucleic acid sequence inchromatin. Non-limiting examples of enzymatic digestion may includerandom or sequence specific enzymatic digestion using restrictionenzymes, nucleases, combinations of restriction enzymes and nucleases,or combinations of nicking and other nucleases such as NEBNext™fragmentase, which comprises a nicking enzyme that randomly generatesnicks in double stranded DNA and another enzyme that cuts the strandopposite to the generated nicks.

In other embodiments, a fragment of a chromatin may be generated using aphysical method of fragmenting a chromatin. Non-limiting examples ofphysical fragmenting methods that may be used to fragment a chromatin ofthe invention may include nebulization, sonication, and hydrodynamicshearing. In some embodiments, a fragment of a chromatin may begenerated using nebulization. In other embodiments, a fragment of achromatin may be generated using hydrodynamic shearing. In preferredembodiments, a fragment of a chromatin may be generated usingsonication. During sonication, a sample comprising chromatin issubjected to ultrasonic waves, whose vibrations produce gaseouscavitations in the liquid that shear or break high molecular weightmolecules such as chromatin through resonance vibration. Sonicationmethods that may be used to generate a chromatin of the invention areknown in the art

A fragment of a chromatin of the invention may comprise a nucleic acidsequence fragment and may be about 10, 50, 100, 150, 200, 250, 300, 350,400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050,1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650,1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, 2250,2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850,2900, 2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000bases long or more. In some embodiments, a chromatin of the inventionmay comprise a nucleic acid sequence fragment of about 10, 20, 30, 40,50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190,200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330,340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470,480, 490, or about 500 bases long. In other embodiments, a chromatin ofthe invention may comprise a nucleic acid sequence fragment of about500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630,640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, or about 1000 bases long. In yetother embodiments, a chromatin of the invention may comprise a nucleicacid sequence fragment of about 1000, 1010, 1020, 1030, 1040, 1050,1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170,1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290,1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400, 1410,1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500 baseslong. In other embodiments, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1500, 1510, 1520, 1530, 1540,1550, 1560, 1570, 1580, 1590, 1600, 1610, 1620, 1630, 1640, 1650, 1660,1670, 1680, 1690, 1700, 1710, 1720, 1730, 1740, 1750, 1760, 1770, 1780,1790, 1800, 1810, 1820, 1830, 1840, 1850, 1860, 1870, 1880, 1890, 1900,1910, 1920, 1930, 1940, 1950, 1960, 1970, 1980, 1990, or about 2000bases long. In additional embodiments, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 2000, 2100, 2150,2200, 2250, 2300, 2350, 2400, 2450, or about 2500 bases long. In otherembodiments, a chromatin of the invention may comprise a nucleic acidsequence fragment of about 2000, 2050, 2100, 2150, 2200, 2250, 2300,2350, 2400, 2450, or about 2500 bases long. In still other embodiments,a chromatin of the invention may comprise a nucleic acid sequencefragment of about 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900,2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000 baseslong or more.

In some preferred embodiments, a chromatin fragment of the invention maycomprise a nucleic acid sequence fragment of about 550, 560, 570, 580,590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720,730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860,870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120,1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240,or about 1250 bases long. In a preferred embodiment, a chromatin of theinvention may comprise a nucleic acid sequence fragment of about 750,760, 770, 780, 790, 800, 810, 820, 830, 840, or about 850 bases long. Inanother preferred embodiment, a chromatin of the invention may comprisea nucleic acid sequence fragment of about 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, or about 1050 bases long.

In other preferred embodiments, a chromatin fragment of the inventionmay comprise a nucleic acid sequence fragment of about 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040,1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160,1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280,1290, 1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400,1410, 1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500bases long. In a preferred embodiment, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 950, 960, 970, 980,990, 1000, 1010, 1020, 1030, 1040, or about 1050 bases long. In anotherpreferred embodiment, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1200, 1210, 1220, 1230, 1240,1250, 1260, 1270, 1280, 1290, or about 1300 bases long.

As described in this section above, a chromatin of the invention maycomprise one or more nucleosomes. As such, a chromatin fragment of theinvention may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, or about 20 nucleosomes. In some embodiments, achromatin fragment of the invention may comprise about 1, 2, 3, 4, orabout 5 nucleosomes. In other embodiments, a chromatin fragment of theinvention may comprise about 5, 6, 7, 8, 9, or about 10 nucleosomes. Inyet other embodiments, a chromatin fragment of the invention maycomprise about 10, 11, 12, 13, 14, or about 15 nucleosomes. In otherembodiments, a chromatin fragment of the invention may comprise about15, 16, 17, 18, 19, or about 20 nucleosomes. In preferred embodiments, achromatin fragment of the invention may comprise about 4 nucleosomes. Inother preferred embodiments, a chromatin fragment of the invention maycomprise about 5 nucleosomes.

A target chromatin fragment of the invention may comprise a structuralor a functional feature of chromatin as described above, a fragment of aphysical or functional feature, or no physical or functional features orknown physical or functional features. In some embodiments, a targetchromatin fragment of the invention comprises a structural feature ofchromatin. In other embodiments, a target chromatin fragment of theinvention comprises no physical or functional features or known physicalor functional features. In yet other embodiments, a target chromatinfragment of the invention comprises a functional feature of chromatin.In exemplary embodiments, a target chromatin is a promoter.

(c) Tagging the Target Chromatin

According to the invention, a target chromatin from a first cell sampleis tagged and a target chromatin from a second cell sample is nottagged. In essence, tagging a target chromatin may comprise contactingthe target chromatin of the invention with a tag capable of specificallyrecognizing and binding one or more portions of a target chromatin. Asused herein, “specifically recognizing” refers to a binding reactionbetween two separate molecules that is at least two times the backgroundand more typically more than 10 to 100 times the background molecularassociations under physiological conditions. A tag may be capable ofspecifically recognizing and binding 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10components of a target chromatin. In preferred embodiments, a tag iscapable of specifically recognizing and binding one component of atarget chromatin. Alternatively, not tagging a target chromatin maycomprise contacting the target chromatin with a non-functional tag thatis not capable of specifically recognizing and binding one or moreportions of the target chromatin. Specifically, the non-functional taglacks a component of the tag that is essential for specificallyrecognizing and thus tagging the target chromatin.

A tag may be capable of specifically recognizing and binding a componentin a target chromatin. A component in a target chromatin may be anucleic acid sequence in a nucleic acid associated with a targetchromatin, a protein associated with a target chromatin, or a chromatinstructural or functional feature in a target chromatin. A nucleic acidsequence associated with a target chromatin that may be specificallyrecognized and bound by a tag of the invention may be a nucleic acidsequence normally found in a chromatin of a cell of the invention.

Individuals of ordinary skill in the art will recognize that anexogenous component introduced into a cell to facilitate tagging atarget chromatin of the invention cannot and will not disrupt a targetchromatin, or a structural or functional feature of a target chromatin.Methods of designing a chromatin component and a tag capable of bindingthe chromatin component that does not disrupt a chromatin of theinvention may depend on the particular application of a method of theinvention, and may be determined experimentally. For instance, if anapplication of a method of the invention comprises promoter function, atag may be designed to bind anywhere adjacent to the promoter, butwithout disrupting the promoter.

In an embodiment, a tag of the invention comprises a nucleic acidsequence capable of binding a nucleic acid sequence component of atarget chromatin, wherein the nucleic acid sequence component of thechromatin is normally present in a cell of the invention. Non-limitingexamples of nucleic acids capable of binding a nucleic acid sequencecomponent of a chromatin include antisense RNA or DNA nucleic acids, andmodified nucleic acids and nucleic acid mimics such as peptide nucleicacids, locked nucleic acids, phosphorodiamidate morpholino oligomers(PMO). In some embodiments, a tag of the invention comprises a nucleicacid sequence comprising locked nucleotides. For instance, a nucleicacid sequence comprising locked nucleotides may be as described inUS20110262908 or US20120040857, and a peptide nucleic acid tag may be asdescribed in Boffa et al. 1995 PNAS 92:1901-1905, the disclosures of allof which are incorporated herein in their entirety. Importantly, anon-functional tag of the invention lacks the nucleic acid component ofthe tag such that the non-functional tag is not capable of specificallyrecognizing a nucleic acid sequence component of a target chromatin.

In specific embodiments, a tag of the invention comprises a guide RNA(gRNA) capable of binding a nucleic acid sequence component of achromatin, wherein the nucleic acid sequence component of the chromatinis normally present in a cell of the invention. A gRNA may be part ofthe Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)Type II system. There are two distinct components to this system: (1) aguide RNA and (2) an endonuclease, in this case the CRISPR associated(Cas) nuclease, Cas9. The guide RNA is a combination of the endogenousbacterial crRNA and tracrRNA into a single chimeric guide RNA (gRNA)transcript. The gRNA combines the targeting specificity of the crRNAwith the scaffolding properties of the tracrRNA into a singletranscript. When the gRNA and the Cas9 are expressed in the cell, thegRNA/Cas9 complex is recruited to the target sequence by thebase-pairing between the gRNA sequence and the complement to the targetsequence in the genomic DNA. For successful binding of Cas9, the genomictarget sequence must also contain the correct Protospacer AdjacentMotiff (PAM) sequence immediately following the target sequence. Thebinding of the gRNA/Cas9 complex localizes the Cas9 to the genomictarget sequence. Accordingly, guide RNA corresponds to a nucleic addcomprising a complementary sequence to a nucleic acid sequence componentof a chromatin. In the present invention, guide RNA is engineered tocomprise a sequence complementary to a portion of a nucleic acidsequence component of a chromatin such that it is capable of targetingthe nucleic acid sequence component of a chromatin. In a particularembodiment, the guide RNA comprises a sequence of 5 to 50 nucleotides,preferably at least 12 nucleotides which is complementary to the nucleicacid sequence component of a chromatin. In a more particular embodiment,the guide RNA is a sequence of at least 30 nucleotides which comprisesat least 10 nucleotides, preferably 12 nucleotides complementary to thenucleic acid sequence component of a chromatin. In certain embodiments,a target nucleic acid sequence comprises a PAM sequence immediatelyfollowing the nucleic acid sequence component of a chromatin. Thetypical length of the nucleic acid sequence component of a chromatin isabout 20 base pairs, although sequences that are longer or shorter canbe used.

A tag of the invention further comprises a protein that associates withthe nucleic add portion of the tag. Accordingly, a tag further comprisesa protein capable of binding the nucleic acid portion of the tag,wherein the nucleic acid portion of the tag specifically recognizes anucleic acid sequence normally found in a cell of the invention. Theprotein may be a wild type nucleic acid binding protein capable ofbinding a nucleic acid tag bound to a target chromatin. Alternatively,the protein may be engineered to have binding specificity for thenucleic acid portion of the tag. In preferred embodiments, the proteincomprises a nuclease inactivated Cas9 protein, or derivatives thereof,wherein the Cas9 protein binds to the nucleic acid portion of the tag ofthe invention. In exemplary embodiments, a tag comprises Cas9, whereinCas9 binds to guide RNA (gRNA). Importantly, the non-functional tagcomprises the same protein as the functional tag of the invention.

A tag of the invention further comprises an affinity handle. An affinityhandle may be used as an affinity purification handle for purifying atagged target chromatin. Affinity handles may include any affinityhandle for which a cognate binding agent is readily available. Anaffinity handle may be an aptamer, an antibody, an antibody fragment, adouble-stranded DNA sequence, modified nucleic acids and nucleic acidmimics such as peptide nucleic acids, locked nucleic acids,phosphorodiamidate morpholino oligomers (PMO), a ligand, a ligandfragment, a receptor, a receptor fragment, a polypeptide, a peptide, acoenzyme, a coregulator, an allosteric molecule, non-immunoglobulinscaffolds such as Affibodies, Anticalins, designed Ankyrin repeatproteins and others, an ion, or a small molecule for which a cognatebinding agent is readily available. The term “aptamer” refers to apolypeptide or a polynucleotide capable of binding to a target moleculeat a specific region. It is generally accepted that an aptamer, which isspecific in its binding to any polypeptide, may be synthesized and/oridentified by in vitro evolution methods. Non limiting examples ofhandles that may be suitable for isolating a chromatin may includebiotin or a biotin analogue such as desthiobiotin, digoxigenin,dinitrophenol or fluorescein, a macromolecule that binds to a nucleicacid or a nucleic acid binding protein such as the Lac repressor, a zincfinger protein, a transcription activator protein capable of binding anucleic acid, or a transcription activator-like (TAL) protein, antigenicpolypeptides such as protein A, or peptide ‘tags’ such as polyhistidine,FLAG, HA and Myc tags. In preferred embodiments, an affinity handle maybe an antigenic polypeptide. In specific embodiments, an affinity handlemay be the protein A antigenic polypeptide, or derivatives thereof. Dueto the properties of an affinity handle, the affinity handle may alsonon-specifically associate with nucleic acid binding proteins.Importantly, the non-functional tag comprises the same affinity handleas the functional tag of the invention.

In specific embodiments, a tag of the invention comprises protein A asthe affinity handle. In other specific embodiments, a tag of theinvention comprises catalytically inactive Cas9 nuclease as the protein.In exemplary embodiments, a tag of the invention comprises protein A anda catalytically inactive Cas9 nuclease. In another exemplary embodiment,a tag of the invention comprises protein A tagged nuclease inactivatedCas9 protein and a gRNA which has been modified to bind a nucleic acidsequence normally found in a cell. In still another exemplaryembodiment, a non-functional tag of the invention comprises protein Atagged nuclease inactivated Cas9 protein and does not comprise a gRNA.The Cas9 and gRNA of the invention may be components of the CRISPRsystem as discussed above.

A target chromatin may be contacted with a tag or non-functional tag atany time during a method of the invention leading to isolation of targetchromatin. For instance, a target chromatin may be contacted with a tagor non-functional tag during cell culture by expressing the tag ornon-functional tag in a cell of the invention. Alternatively, a targetchromatin may be contacted with a tag or non-functional tag after cellculture but before cell lysis, after cell lysis, or after fragmentationof chromatin to generate chromatin fragments comprising a targetchromatin. In such embodiments, a tag or non-functional tag may be addedto the cell culture or cell lysate as a recombinant protein. Therecombinant protein may be expressed, isolated and purified via methodsstandard in the art for protein purification.

In some embodiments, a target chromatin is contacted with a tag ornon-functional tag after cell culture but before cell lysis. As such, atag or non-functional tag may be introduced into a cell before celllysis. Methods of introducing a tag or non-functional tag into a cell ofthe invention can and will vary depending on the type of cell, the tag,and the application of a method of the invention. For instance, anucleic acid (i.e. a plasmid) capable of expressing a tag ornon-functional tag of the invention may be introduced into a cell afterculture such that the tag or non-functional tag is expressed during cellculture. In other embodiments, a target chromatin is contacted with atag or non-functional tag after cell lysis. In yet other embodiments, atarget chromatin is contacted with a tag or non-functional tag aftercell lysis and chromatin fragmentation. In both of the foregoingembodiments, the tag or non-functional tag may be introduced as arecombinant protein. In specific embodiments, a target chromatin iscontacted with a tag or non-functional tag during cell culture byexpressing the tag or non-functional tag in a cell of the inventionduring cell culture. In an exemplary embodiment, a target chromatin iscontacted with a tag during cell culture by expressing a tag comprisinga gRNA, inactivated Cas9, and an affinity handle in a cell of theinvention during cell culture. In another exemplary embodiment, a targetchromatin is contacted with a non-functional tag during cell culture byexpressing a tag comprising an inactivated Cas9 and an affinity handlein a cell of the invention during cell culture, wherein thenon-functional tag does not comprise a gRNA.

(d) Preparation of Cell Lysate

According to the invention, affinity handle bound to a tagged targetchromatin bound to nucleic acid binding proteins and affinity handlebound to non-specific nucleic acid binding proteins in a first cellsample is isolated and affinity handle bound to non-specific nucleicacid binding proteins in a second cell sample is isolated. The method ofisolating affinity handle in a first cell sample and second cell samplemay be performed on a cell lysate derived from a cell sample. A skilledpractitioner of the art will appreciate that structural and functionalfeatures of an affinity handle and a tagged target chromatin must bepreserved during cell lysis and isolation of the affinity handle and thetagged target chromatin. The association of proteins with a taggedtarget chromatin may be preserved during cell lysis using methods knownin the art for preserving a complex of proteins with a nucleic acidsequence. For instance, lysing of a cell may be performed underrefrigeration or using cryogenic methods and buffer conditions capableof preserving association of proteins and nucleic acid sequences. Inaddition, a complex of proteins with a nucleic acid may be preserved bycrosslinking protein and nucleic acid complexes in a cell prior tolysing. Crosslinking protein and nucleic acid complexes in a cell mayalso capture, or preserve, transient protein-protein and protein-nucleicacid interactions.

In some embodiments, a complex of proteins with a nucleic acid may bepreserved by crosslinking protein and nucleic acid complexes in achromatin prior to lysing a cell and isolating the affinity handle andtarget chromatin. Crosslinking is the process of joining two or moremolecules such as two proteins or a protein and a nucleic acid molecule,by a covalent bond. Molecules may be crosslinked by irradiation withultraviolet light, or by using chemical crosslinking reagents. Chemicalcrosslinking reagents capable of crosslinking proteins and nucleic acidsare known in the art and may include crosslinking reagents that targetamines, sulfhydryls, carboxyls, carbonyls or hydroxyls; omobifunctionalor heterobifunctional crosslinking reagent, variable spacer arm lengthor zero-length crosslinking reagents, cleavable or non-cleavablecrosslinking reagents, and photoreactive crosslinking reagents.Non-limiting examples of crosslinking reagents that may be used tocrosslink protein complexes and/or protein complexes and nucleic acidsmay include formaldehyde, glutaraldehyde, disuccinimidyl glutarate,disuccinimidyl suberate, a photoreactive amino acid such asphoto-leucine or photo-methionine, and succinimidyl-diazirine. Thedegree of crosslinking can and will vary depending on the application ofa method of the invention, and may be experimentally determined.

In a preferred embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehyde.In an exemplary embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehydeas described in the examples.

A skilled practitioner of the art will appreciate that protocols forlysing a cell can and will vary depending on the type of cell, thetarget chromatin of the invention, and the specific application of amethod of the invention. Non-limiting examples of methods that may beused to lyse a cell of the invention may include cell lysis using adetergent, an enzyme such as lysozyme, incubation in a hypotonic bufferwhich causes a cell to swell and burst, mechanical disruption such asliquid homogenization by forcing a cell through a narrow space,sonication, freeze/thaw, mortar and pestle, glass beads, andcombinations thereof. In some embodiments, when a cell of the inventionis a yeast cell, the cell may be cryogenically lysed under liquidnitrogen temperature with glass beads. In exemplary embodiments, when acell of the invention is a yeast cell, the cell may be cryogenicallylysed under liquid nitrogen temperature with glass beads as described inthe examples.

Buffer conditions used during lysing and isolation of a chromatin of theinvention can and will be altered to control stringent conditions duringcell lysis and isolation to preserve association of proteins and nucleicacid sequences of a chromatin. “Stringent conditions” in the context ofchromatin isolation are conditions capable of preserving specificassociation of proteins and nucleic acids of a chromatin, but minimizingnon-specific association of proteins and nucleic acids. Stringentcondition can and will vary depending on the application of a method ofthe invention, the target chromatin of the invention, the nucleic acidsequence in a target chromatin, the proteins or protein complexesassociated with a target chromatin of the invention, whether or notproteins, protein complexes and nucleic acid sequences are crosslinked,and the conditions used for crosslinking proteins, protein complexes andnucleic acid sequences of a target chromatin. For instance, morestringent buffer conditions may be used in a method of the inventionwherein proteins, protein-protein complexes, and protein-nucleic acidcomplexes are crosslinked compared to a method of the invention whereinproteins, protein-protein complexes, and protein-nucleic acid complexesare not crosslinked. As such, stringent buffer conditions used duringcell lysis and isolation of a nucleic acid sequence of the invention maybe experimentally determined for each application wherein a method ofthe invention is used. Buffer conditions that may alter stringentconditions during cell lysis and isolation may include pH and saltconcentration. In preferred embodiments, proteins, protein-proteincomplexes, and protein-nucleic acid complexes of a target chromatin ofthe invention are crosslinked, and stringent buffer conditions are usedduring lysis and isolation of a chromatin of the invention. In exemplaryembodiments, proteins, protein-protein complexes, and protein-nucleicacid complexes of a target chromatin of the invention are crosslinked,and stringent buffer conditions are used during lysis and isolation of achromatin of the invention and are as described in the examples. In anexemplary embodiment, a first cell sample and a second cell sample arecrosslinked to stabilize protein-protein and protein-nucleic acidinteractions with a target chromatin, then the first cell sample and thesecond cell sample are lysed, and then the target chromatin in the firstcell sample and the second cell sample is fragmented resulting in 500 to1500 base pair fragments.

(e) Chromatin Isolation

According to the invention, the method of isolating an affinity handlefrom each cell sample may be performed on cell lysates derived from thecell samples. As described in Sections III(d) above, a cell lysatecomprises a lysate of a cell sample, wherein a target chromatin istagged in one of the lysates, or one of the cell samples. A cell lysatealso comprises a lysate of a cell sample, wherein a target chromatin isnot tagged in one of the lysates, or one of the cell samples.

Isolating an affinity handle may enrich for a tagged target chromatin.An affinity handle bound to a tagged target chromatin may be isolatedfrom a mixture of chromatins or chromatin fragments in a cell lysate. Asused herein, the term “isolated” or “purified” may be used to describe apurified preparation of a target chromatin that is enriched for thetarget chromatin, but wherein the target chromatin is not necessarily ina pure form due to the presence of non-specifically bound nucleic acidbinding proteins. A target chromatin of the present invention may bepurified to homogeneity or other degrees of purity. In general, thelevel of purity of an isolated target chromatin can and will varydepending on the cell type, the specific chromatin to be isolated, andthe intended use of a target chromatin of the invention. The level ofpurity of an isolated target chromatin may be determined using methodsknown in the art. For instance, the level of purity of an isolatedtarget chromatin may be determined by determining the level of purity ofa nucleic acid sequence associated with a target chromatin, bydetermining the level of purity of a protein associated with a targetchromatin, or by determining the level of enrichment of a targetchromatin, compared to a non-target chromatin in a cell. In preferredembodiments, the level of purity of an isolated target chromatin isdetermined by determining the level of enrichment of a target chromatin,compared to a non-target chromatin in a cell.

For example, an isolated target chromatin is not necessarily 100% pure,but may be about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. Anisolated target chromatin may be enriched for the target chromatin,relative to a chromatin in the lysed preparation that was contacted witha non-functional tag of the invention. An isolated target chromatin maybe enriched by 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fold relative to achromatin that was contacted with a non-functional tag of the invention.In some embodiments, an isolated target chromatin is enriched by 10, 20,30, 40 or 50 fold relative to a chromatin that was contacted with anon-functional tag of the invention. In other embodiments, an isolatedtarget chromatin is enriched by 50, 60, 70, 80, 90, or 100 fold relativeto a chromatin that was contacted with a non-functional tag of theinvention. In an exemplary embodiment, an isolated target chromatin isenriched 60, 65, 70, 75 or 80 fold relative to a chromatin that wascontacted with a non-functional tag of the invention.

An affinity handle may be isolated using methods known in the art, suchas electrophoresis, molecular, immunological and chromatographictechniques, ion exchange, hydrophobic, affinity, and reverse-phase HPLCchromatography, size exclusion chromatography, precipitation, dialysis,chromatofocusing, ultrafiltration and diafiltration techniques, andcombinations thereof. For general guidance in suitable purificationtechniques, see Scopes, R., Protein Purification, Springer-Vertag, NY(1982).

In general, a method of the invention comprises isolating an affinityhandle by affinity purification, or affinity purification in combinationwith other methods of isolating chromatin described above. In apreferred embodiment, a method of the invention comprises isolating anaffinity handle by affinity purification. Non limiting examples ofaffinity purification techniques that may be used to isolate an affinityhandle may include affinity chromatography, immunoaffinitychromatography, size exclusion chromatography, and combinations thereof.See, for example, Roe (ed), Protein Purification Techniques: A PracticalApproach, Oxford University Press, 2nd edition, 2001.

A target chromatin contacted and bound by a tag may be isolated usingany affinity purification method known in the art. In short, a targetchromatin is bound to an affinity handle capable of binding to asubstrate. The substrate comprising a bound affinity handle bound totarget chromatin may then be washed to remove non-target chromatin andother cell debris, and the target chromatin may be released fromsubstrate. Methods of affinity purification of material comprising anaffinity handle are known in the art and may include binding theaffinity handle to a substrate capable of binding the affinity handle.The substrate may be a gel matrix such as gel beads, the surface of acontainer, or a chip. The target chromatin bound to the affinity handlemay then be purified. Methods of purifying tagged molecules are known inthe art and will vary depending on the target molecule, the tag, and thesubstrate. For instance, if the affinity handle is bound to a targetchromatin, the affinity handle may be bound to a magnetic bead substratecomprising IgG, and purified using a magnet. Importantly, thenon-functional tag comprising an affinity handle in the second cellsample is subjected to the same affinity purification method as thefirst cell sample.

(f) Protein Extraction, Identification, and Determination of Labeling

Proteins and peptides associated with an isolated tagged targetchromatin are extracted from the isolated tagged target chromatin.Methods of extracting proteins from chromatin are generally known in theart of protein biochemistry. Generally, any extraction protocol suitablefor isolating proteins and known to those of skill in the art may beused. Extracted proteins may also be further purified before proteinidentification. For instance, protein extracts may be further purifiedby differential precipitation, differential solubilization,ultracentrifugation, using chromatographic methods such as sizeexclusion chromatography, hydrophobic interaction chromatography, ionexchange chromatography, affinity chromatography, metal binding,immunoaffinity chromatography, HPLC, or gel electrophoriesis such asSDS-PAGE and QPNC-PAGE. In a preferred embodiment, extracted proteinsare further purified using SDS-PAGE.

Extracted and purified intact proteins and post-translationalmodification of proteins may then be identified. Alternatively,extracted and purified intact proteins may be further digested, and theresulting peptide fragments are identified. In some embodiments, intactextracted proteins are identified. In preferred embodiments, extractedproteins are further digested, and the resulting peptide fragments areidentified. For instance, protein extracts may be fragmented byenzymatically digesting the proteins using a protease such as trypsin.In exemplary embodiments, extracted proteins are further digested asdescribed in the examples.

Methods of identifying proteins or protein fragments are known in theart and may include mass spectrometry (MS) analysis, or a combination ofmass spectrometry with a chromatographic technique. Non limitingexamples of mass spectrometer techniques may include tandem massspectrometry (MS/MS), matrix-assisted laser desorption/ionization sourcewith a time-of-flight mass analyzer (MALDI-TOF), inductively coupledplasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS),thermal ionization-mass spectrometry (TIMS), isotope ratio massspectrometry (IRMS), and spark source mass spectrometry (SSMS).Chromatographic techniques that may be used with MS may include gaschromatography, liquid chromatography, and ion mobility spectrometry. Ina preferred embodiment, proteins may be identified using tandem massspectrometry in combination with liquid chromatography (LC-MS/MS). Inanother preferred embodiment, post-translational modification ofproteins may be identified using tandem mass spectrometry in combinationwith liquid chromatography (LC-MS/MS).

In the present invention, the method of label-free proteomics is used tocategorize whether proteins enriched with a section of chromatin arespecific or contaminant. Label-free methods of quantifying proteins orprotein fragments are known in the art. In label-free quantitativeproteomics, each sample is separately prepared, then subjected toindividual methods of identifying proteins or protein fragments whichmay include LC-MS/MS or LC/LC-MS/MS. According to the invention, onesample comprises a target chromatin that is tagged in the cell sampleand one sample comprises a target chromatin that is untagged in the cellsample. Label-free protein quantification is generally based on twocategories of measurement. In the first are the measurements of ionintensity changes such as peptide peak areas or peak heights inchromatography. The second is based on the spectral counting ofidentified proteins after MS/MS analysis. Peptide peak intensity orspectral count is measured for individual LC-MS/MS or LC/LC-MS/MS runsand changes in protein abundance are calculated via a direct comparisonbetween different analyses. In a preferred embodiment, the proteinsidentified using mass spectrometry are quantified and identified asenriched in the sample containing the tagged target chromatin comparedto the sample containing the untagged target chromatin using label-freeproteomics. In an exemplary embodiment, the proteins identified usingmass spectrometry are quantified and identified as enriched in thesample containing the tagged target chromatin compared to the samplecontaining the untagged target chromatin using spectral counting.

The method of protein quantification by spectral count is known in theart and is reviewed in Zhu et al., J Biomed Biotechnol 2010, which isincorporated by reference herein. In spectral counting, relative proteinquantification is achieved by comparing the number of identified MS/MSspectra from a protein of one sample to the same protein in the othersample. In the present invention, one sample comprises a targetchromatin that is tagged and another sample comprises a target chromatinthat is untagged. Protein quantification in spectral counting utilizesthe fact that an increase in protein abundance typically results in anincrease in the number of its proteolytic peptides, and vice versa. Thisincreased number of (tryptic) digests then usually results in anincrease in protein sequence coverage, the number of identified uniquepeptides, and the number of identified total MS/MS spectra (spectralcount) for each protein.

As such, determining the abundance of an identified protein in a taggedchromatin sample compared to the same protein in an untagged chromatinsample, may determine if the protein was specifically associated with atarget chromatin of the invention. If an identified protein associatedwith a target chromatin is in enriched in a tagged chromatin samplecompared to the same protein in an untagged chromatin sample, then theprotein was specifically associated with a target chromatin of theinvention. If an identified protein is not enriched in a taggedchromatin sample compared to an untagged chromatin sample, then theprotein is non-specifically associated with a target chromatin of theinvention.

A skilled artisan in spectral counting will appreciate thatnormalization and statistical analysis of spectral counting datasets arenecessary for accurate and reliable detection of protein changes. Sincelarge proteins tend to contribute more peptide/spectra than small ones,a normalized spectral abundance factor (NSAF) is defined to account forthe effect of protein length on spectral count. NSAF is calculated asthe number of spectral counts (SpC) identifying a protein, divided bythe protein's length (L), divided by the sum of SpC/L for all proteinsin the experiment. NSAF allows the comparison of abundance of individualproteins in multiple independent samples and has been applied toquantify the expression changes in various complexes.

In the present invention, to measure enrichment of a protein, thenormalized spectral abundance factor (NSAF) is calculated for eachprotein in each lane of an SDS-PAGE gel by dividing the number ofspectral counts (normalized for the size of the protein) of a givenprotein by the sum of all normalized spectral counts of all proteins inthe gel lane. The enrichment level for each protein is identified bycalculating the fold enrichment (tagged chromatin/untagged chromatin)using the NSAF values. In an exemplary embodiment, proteins enriched ina sample containing a tagged target chromatin compared to a samplecontaining an untagged target chromatin are enriched by at least about 2fold. In other embodiments, proteins enriched in a sample containing atagged target chromatin compared to a sample containing the untaggedtarget chromatin are enriched by at least about 1.5 fold. In otherembodiments, proteins enriched in a sample containing a tagged targetchromatin compared to a sample containing an untagged target chromatinare enriched by at least about 3 fold, about 4 fold, about 5 fold, about6 fold, about 7 fold, about 8 fold, about 9 fold, about 10 fold, about11 fold, about 12 fold, about 13 fold, about 14 fold, about 15 fold,about 16 fold, about 17 fold, about 18 fold, about 19 fold or about 20fold. As such, a protein enriched by at least about 2 fold in a taggedchromatin sample compared to an untagged chromatin sample, isspecifically associated with the chromatin. For instance, a baseline fornon-specifically associated proteins may be proteins enriched by lessthan about 1.5 fold in a tagged chromatin sample compared to an untaggedchromatin sample, wherein one or more proteins are not associated withchromatin. Non-limiting examples of proteins not associated with achromatin may include enzymes required for metabolism, receptors, andribosomal proteins. In preferred embodiments, proteins not associatedwith a chromatin are ribosomal proteins, and a baseline fornon-specifically associated proteins is an enrichment less than about1.5 fold in a tagged chromatin sampled compared to an untagged chromatinsample. In an exemplary embodiment, proteins or protein fragmentsenriched by at least 15 fold in a tagged chromatin sample compared to anuntagged chromatin sample are specifically associated with a targetchromatin.

In preferred embodiments, a target chromatin is tagged in one cellsample and a target chromatin is not tagged in a second cell sample, andMS analysis is used to identify proteins or protein fragments isolatedduring affinity purification of each sample, and label-free proteomicsis used to determine if a protein or a protein fragment is specificallyor non-specifically associated with the target chromatin. Methods ofderiving MS data to identify proteins or protein fragments are known inthe art, and may include using known computational techniques to distillMS data such as Mascot Distiller, Rosetta Elucidator, and MaxQuant. Insome embodiments, MS data is derived using Rosetta Elucidator. In otherembodiments, MS data is derived using MaxQuant. In preferredembodiments, MS data is derived using Mascot Distiller.

IV. Applications

A method of the invention may be used for any application wherein adetermination of chromatin structure or function may be required. Forinstance, a method of the invention may be used to determinerearrangement in chromatin structure, genome metabolism, epigeneticregulatory mechanisms, transient association of proteins with chromatin,initiation or silencing of expression of a nucleic acid sequence,identify proteins transiently associated with a chromatin, orpost-translational modification of proteins associated with a chromatinor chromatin rearrangement. An application of a method of the inventionmay include determining changes in chromatin function and structure inresponse to changing growth conditions, exposure to a drug or smallmolecule, or during stages of cell cycles.

A method of the invention may also be used to determine proteinslocalized to a target chromatin associated with a specific diseasestate. For example, a biological sample may be obtained from a subjectwith a specific disease and a biological sample may be obtained from asubject without a specific disease. A method of the invention may beperformed on each of the biological samples. The difference in proteinsassociated with the target chromatin between the disease sample and thenon-disease sample may then be compared. Such a method allows thedetermination of proteins localized to a target chromatin associatedwith a specific disease state. In certain embodiments, the disease maybe cancer. The information gleaned from the foregoing method may be usedto identify potential targets for drug development.

Additionally, a method of the invention may be used to diagnose adisease. For example, a biological sample may be obtained from a subjectsuspected of having a specific disease. A method of the invention may beperformed on the biological sample. The identification of proteinsspecifically associated with a target chromatin may be compared to areference sample, wherein when the reference sample is from a diseasedsubject, the proteins specifically associated with a target chromatinare the same or wherein when the reference sample is from a non-diseasedsubject, the proteins specifically associated with a target chromatinare different, then the subject may be diagnosed with the disease.

Further, a method of the invention may be used to map the 4Darchitecture of chromatin. Accordingly, a method of the invention may beused to study regions of chromosomes that come in contact with eachother. Additionally, a method of the invention may be used to understandthe proteins involved in chromosomal architecture.

In some embodiments, a method of the invention is used to determinedifferences in chromatin structure and function between atranscriptionally silent and a transcriptionally active state of agenomic locus. As such, proteins specifically associated with a genomiclocus, and post-translational modifications of proteins associated witha chromatin comprising the genomic locus may be determined in cellscomprising a transcriptionally silent state of a genomic locus, and incells comprising a transcriptionally active state of a genomic locus.

V. Kits

In other aspects, the present invention provides kits for isolating andidentifying proteins specifically associated with a chromatin. The kitsmay comprise, for example, a growth medium comprising a metabolic label,or a metabolic label that may be added to a growth medium, and cellscomprising a tagged target chromatin, and instructions describing amethod of the invention. A kit may further comprise material necessaryfor affinity purification of a tagged target chromatin, and a samplecomprising metabolically labeled and unlabeled non-specificallyassociated proteins for determination of a baseline for non-specificallyassociated proteins. A kit my also comprise material necessary foraffinity purification of a tagged target chromatin, and instructionsdescribing a method of the invention.

In other embodiments, a kit may comprise a protein A-tagged TAL proteinengineered to bind a target chromatin. In alternative embodiments, a kitmay comprise a vector for expressing a protein A-tagged TAL protein,wherein the TAL protein may be engineered to bind a target chromatin.

In still other embodiments, a kit may comprise an affinity handle-taggedinactivated Cas9 and gRNA engineered to bind a target chromatin. A kitmay comprise nucleic acids suitable for expressing an affinityhandle-tagged inactivated Cas9 and gRNA engineered to bind a targetchromatin or cells comprising nucleic acids suitable for expressing anaffinity handle-tagged inactivated Cas9 and gRNA engineered to bind atarget chromatin. A kit may also comprise instructions for expressingand purifying an affinity handle-tagged inactivated Cas9 and gRNAengineered to bind a target chromatin. In each of the foregoingembodiments, a kit may further comprise an affinity handle-taggedinactivated Cas9 without a gRNA for use as a control.

Cells and methods of the invention may be as described in Section I,Section II, and Section III above.

EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples that follow representtechniques discovered by the inventors to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Introduction for Examples 1-3

It has long been appreciated that chromatin-associated proteins andepigenetic factors play central roles in cell-fate reprogramming ofgenotypically identical stem cells through lineage-specifictranscription or repression of precise genes and large chromosomalregions (Martin, 1981; Ho and Crabtree, 2010; Rossant, 2008). However,the hierarchy of chromatin-templated events orchestrating the formationand inheritance of different epigenetic states remains poorly understoodat a molecular level. Since misregulation of chromatin structure andpost-translational modification of histones (PTMs) is linked to cancerand other epigenetic diseases (Jones and Baylin, 2007; Chi et al.,2010), it is imperative to establish new methodologies that will allowcomprehensive studies and unbiased screens for participants inepigenetic mechanisms. Unfortunately, defining how chromatin regulatorscollectively assemble and operate on a precise region of the genome isdifficult to elucidate; there are no current methodologies that allowfor determination of all proteins present at a defined, small region ofchromatin.

Technical challenges have precluded the ability to determine positioningof chromatin factors along the chromosome. Chromatin immunoprecipitation(ChIP) assays have been used to better understand genome-widedistribution of proteins and histone modifications within a genome atthe nucleosome level (Dedon at al., 1991; Ren et al., 2000; Pokholok etal., 2005; Robertson et al., 2007; Johnson et al., 2007; Barski et al.,2007; Mikkelsen et al, 2007). However, major drawbacks of ChIP-basedchromatin enrichment methods include experiments that are largelyconfined to examining singular histone PTMs or proteins rather thansimultaneous profiling of multiple targets, the inability to determinethe co-occupancy of particular histone PTMs, and that ChIP is reliant onthe previous identification of the molecular target. Affinitypurification approaches have been devised for the isolation of achromatin region (Griesenbeck et al., 2003; Agelopoulos et al., 2012);however, these approaches were not done at a level for proteomicanalysis and they do not provide a mechanism for determining thespecificity of protein interactions. More recently, groups biochemicallyenriching for intact chromatin have reported characterization ofproteins associated with large chromatin structures such as telomeres(Dejardin and Kingston, 2009) and engineered plasmids (Akiyoshi et al.,2009; Unnikrishnan et al., 2010); however, these approaches do notenrich for a small integrated genomic locus and do not employspecialized mass spectrometric techniques to detect proteincontamination in purified material.

We sought to compare differences in chromatin between thetranscriptionally active and silent states of a single genomic locus,and developed a technology, called chromatin affinity purification withmass spectrometry (ChAP-MS). ChAP-MS provides for the site-specificenrichment of a given ˜1,000 base pair section of a chromosome followedby unambiguous identification of both proteins and histone PTMsassociated with this chromosome section using highly selective massspectrometry. Using ChAP-MS, we were able to purify chromatin at theSaccharomyces cerevisiae GAL.1 locus in transcriptionally silent andactive states. We identified proteins and combinatorial histone PTMsunique to each of these functional states and validated these findingswith ChIP. The ChAP-MS technique will greatly improve the field ofepigenomics as an unbiased approach to study regulatory mechanisms onchromatin.

Example 1 ChAP-MS Technology

FIG. 1A provides an overview of the ChAP-MS approach that was used toscreen for proteins and histone PTMs associated with a specific genomiclocus in transcriptionally active or repressive states. A LexA DNAbinding site was engineered immediately upstream of the GAL1 start codonin a S. cerevisiae strain constitutively expressing a LexA-Protein A(LexA-PrA) fusion protein. The LexA DNA binding site directs thelocalization of the LexA-PrA protein affinity “handle” to the GAL1promoter in vivo. The positioning of the LexA DNA was designed tospecifically enrich for chromatin-associated proteins and histone PTMsregulating gene expression near the transcriptional start site of GAL1.This strain was cultured in glucose to repress gene transcription, orgalactose to activate gene transcription. Following in vivo chemicalcrosslinking to preserve the native protein-protein interactions at GAL1promoter chromatin, the chromatin was sheared to ˜1,000 base pairsections. The PrA moiety of the LexA-PrA fusion protein was then used toaffinity purify the ˜1,000 base pair section of chromatin at the 5′ endof the GAL1 gene for high resolution mass spectrometric identificationof proteins and histone PTMs. It was anticipated that culturing thesecells in glucose would result in the isolation of proteins and PTMscorrelated to silent chromatin, while culturing cells in the presence ofgalactose would purify histone PTMs and proteins, like RNA polymerase,that are involved with active gene transcription.

The GAL1 gene is present at one copy per haploid cell; due to therelative low abundance of the targeted chromatin region in cellularlysates, it was fully anticipated that proteins nonspecificallyassociating with GAL1 chromatin would complicate analysis of theresulting purified material. Copurification of nonspecificallyassociating proteins is one of the major complications of affinitypurifications; however, isotopic labeling of media provides a means togauge in vivo protein-protein interactions and quantitate differences inpeptide abundance (Smart et al., 2009; Tackett et al., 2005a). Theinventors had previously developed a variation of this labelingtechnique called iDIRT (isotopic differentiation of interactions asrandom or targeted) that provides a solution for determining whichcoenriched proteins are specifically or nonspecifically associated witha complex of proteins (Smart et al., 2009; Tackett et al., 2005a). TheiDIRT technique was adapted (as described in FIG. 1B) to control forproteins nonspecifically enriching with LexA-PrA and the resin. By usingthis adaptation of iDIRT on chromatin enriched from active and repressedchromatin states, the proteins nonspecifically enriching with theisolated GAL1 chromatin section were identified. The strain containingthe LexA DNA binding site and LexA-PrA fusion protein was cultured inisotopically light media, while a strain lacking the LexA DNA bindingsite (but still containing the LexA-PrA fusion protein) was cultured inisotopically heavy media (¹³C₆ ¹⁵N₂-lysine). Following isolation of thecells, the light and heavy strains were mixed and colysed. The growthand mixing of light/heavy strains was performed separately under glucoseand galactose growth conditions. The affinity purification of the GAL1chromatin was performed from this mixture of light/heavy lysates.Proteins and histone PTMs specifically associated with the GAL1chromatin containing the LexA DNA binding site were isotopically lightas they arose from the cells grown in light media. Proteins that werenonspecific to the purification were a 1:1 mix of light and heavy asthey were derived equally from the light and heavy lysates. Analysis ofpeptides from the enriched proteins with high-resolution massspectrometry was used to determine the level of isotopically light andheavy proteins, thereby determining whether the detected protein waseither a specific in vivo constituent of GAL1 chromatin or a nonspecificcontaminant.

Example 2 Affinity Purification of a Specific Chromosome Section

To provide for enrichment of a specific chromosome section, a DNAaffinity handle was engineered at the GAL1 gene in S. cerevisiae (FIG.2A). A LexA DNA binding site was inserted via homologous recombinationjust upstream of the GAL1 start codon to create strain LEXA::GAL1. Tocreate this strain, GAL1 was genomically deleted with URA3 in the W303abackground, and then the GAL1 gene was reinserted with the upstream LEXADNA sequence by homologous recombination. A plasmid constitutivelyexpressing LexA-PrA was introduced into the strain to create LEXA::GAL1pLexA-PrA (FIG. 2A). This strain provides a DNA affinity handle at theGAL1 gene and a protein affinity handle for specific enrichment. Todetermine if insertion of this LexA DNA binding site at GAL1 affectedgene transcription, LEXA::GAL1 pLexA-PrA was cultured in glucose torepress gene transcription at GAL1, and separately in galactose toactivate transcription. From these growths, cDNA was prepared andreal-time PCR was used to measure the activation of GAL1 transcriptionin the presence of galactose (FIG. 2B). Insertion of the LexA DNAbinding site just upstream of the GAL1 start codon did not drasticallyaffect the activation of gene transcription; thus, this strain was usedfor ChAP-MS purification of GAL1 chromatin in the transcriptionallyactive and silent states.

To determine the effectiveness of isolation of GAL1 chromatin, thestringency and specificity of different purification conditions wasanalyzed. Purification of protein complexes under increasingstringencies such as high salt levels provides for the isolation offewer nonspecifically interacting proteins (Smart et al., 2009; Tavernaet al., 2006). Since the proteins purified with GAL1 chromatin will bechemically crosslinked, the stringency of the purification canpotentially be quite high. Indeed, ChIP-qPCR against GAL1 showed thatthe PrA-based purification can survive relatively stringent conditions(FIG. 3A). From these studies, 1M NaCl and 1M urea were selected forfuture purifications, as these conditions are quite stringent andprovide for enrichment of the GAL1 chromatin. Using an identical ChIPapproach, the specificity of the GAL1 chromatin enrichment wasdetermined (FIG. 3B). Using primers targeted to the indicated regions ofchromatin surrounding GAL1, it was detected that the first 1,000 basepair section of the GAL/gene was indeed enriched. Enrichment of GAL1chromatin was observed at a similar level under glucose and galactosegrowth conditions (FIG. 3C). The slightly less efficient isolation undergalactose growth conditions may reflect availability of the DNA affinitysite due to alterations in chromatin structure.

Example 3 ChAP-MS Analysis of Transcriptionally Active Anti Silent GAL1Chromatin

Strain LEXA::GAL1 pLexA-PrA was subjected to the ChAP-MS procedure asoutlined in FIG. 1. Strain LEXA::GAL1 pLexA-PrA was grown inisotopically light media, while strain pLexA-PrA was grown inisotopically heavy media. Following growth of each strain to mid-logphase, the cells were treated with 1.25% formaldehyde to trap proteininteractions on the chromosomes. A detailed analysis of the amount offormaldehyde crosslinking required to preserve the in vivo state ofchromatin during affinity purifications was recently published by theinventors (Byrum et al., 2011a, 2011b). Approximately 2.5×10¹¹LEXA::GAL1 pLexA-PrA cells were mixed with an equivalent amount ofisotopically heavy pLexA-PrA cells (separately for media containingglucose and galactose) and then subjected to lysis under cryogenicconditions with a Retch MM301 ball mill (Tackett et al., 2005a). Lysateswere suspended in 20 mM HEPES (pH 7.4), 0.1% Tween 20, 1 M NaCl, 1 Murea, and 2 mM MgCl₂. Lysates were then subjected to sonication andchromatin was sheared to sections of ˜1,000 base pairs. LexA-PrA wascollected on IgG-coated Dynabeads and coenriching proteins were resolvedby SDS-PAGE and visualized by Coomassie staining (FIG. 4A). Gel laneswere sliced into 2 mm sections and subjected to in-gel trypsin digestion(Smart et al., 2009; Tackett et al., 2005a, 2005b). Peptides fromproteins were identified by high-resolution mass spectrometry with aThermo Velos Orbitrap mass spectrometer equipped with a WatersnanoACQUITY UPLC system. Proteins and PTM-containing peptides wereidentified and the level of isotopically light to heavy peptide wascalculated with Mascot Distiller (Smart et al., 2009), Representativespectra are shown in FIG. 4B-D. Major bands observed in the gel lanescorrespond to the affinity purification protein LexA-PrA and IgG chainsas anticipated. Other proteins identified correspond to specifically andnonspecifically enriched proteins. Tables 1 and 2 list the proteinsidentified and percent isotopically light peptides (352 proteins fromthe glucose ChAP-MS and 399 proteins from the galactose ChAP-MS).

Once proteins were identified, a baseline was established fornonspecifically associated proteins in accordance to the iDIRT approach(Smart et al., 2009). Nonspecifically enriching ribosomal proteins wereused to establish the nonspecifically associating baseline (Smart etal., 2009). The average percent isotopically light peptides from 20ribosomal proteins from the glucose and galactose growth conditions wereused to establish this nonspecifically associating baseline (Table 3).This resulted in a nonspecifically associating baseline of 49.93%±2.12%light for the glucose ChAP-MS and 66.8%±7.1% light for the galactoseChAP-MS (FIG. 5). Proteins were categorized as specifically associatingwith GAL1 chromatin if the percent light was greater than 2 SDs abovethe ribosomal level (Smart et al., 2009). FIG. 5 shows the proteins andhistone PTMs specifically enriched with GAL1 chromatin under glucose andgalactose growth conditions. Tables 4 and 5 list proteins that wereidentified as specifically enriched in both the glucose and galactoseChAP-MS analyses. Specifically enriched proteins or histone PTMs knownto be involved in transcriptional regulation are listed in FIG. 5. Forthe glucose and galactose ChAP-MS analyses, 11 and 17 (respectively)additional proteins were detected as specifically enriched (FIG. 5,Tables 4 and 5). These additional proteins are abundant metabolic andheat shock proteins that are typical contaminants and false positivesfor this study. However, narrowing down 352 proteins identified from theglucose ChAP-MS and 399 proteins from the galactose ChAP-MS to 12proteins and 27 proteins/PTMs specifically enriched produced a shortlist of candidates that was easily validated.

The ChAP-MS analyses of GAL1 chromatin revealed association of Gal3,Spt16, Rpb1, Rpb2, H3K14ac, H3K9acK14ac, H3K18acK23ac, H4K5acK8ac, andH4K12acK16ac under transcriptionally active conditions, whiletranscriptionally repressive conditions showed the enrichment ofH3K36me3. In order to validate the ChAP-MS approach, standard ChIP wasperformed to specific interactions detected in the transcriptionallyactive and silent chromatin state at GAL1 (FIG. 6). These ChIPexperiments validated the proteins and PTMs found associated with thetranscriptionally active and repressed states of GAL1 chromatindetermined from the ChAP-MS approach.

Discussion for Examples 1-3

The chromatin biology and epigenomics research communities have beenlimited to biased technologies that restrict targeted genomelocalization studies to previously identified proteins or histone PTMs.Here, a newly developed technology, called ChAP-MS, is described thatcircumvents this limitation by providing for isolation of a ˜1,000 basepair section of a chromosome for proteomic identification ofspecifically bound proteins and PTMs. In essence, the ChAP-MS approachallows one to take a “molecular snapshot” of chromatin dynamics at aspecific genomic locus. Furthermore, employing this approach to targetother chromatin regions will likely provide unprecedented insight on avariety of epigenetic regulatory mechanisms, chromatin structure, andgenome metabolism.

Validation of the ChAP-MS Approach

The ChAP-MS approach was validated on the well-studied GAL1 locus in S.cerevisiae. The GAL1 gene is activated for gene transcription in thepresence of galactose, while glucose represses transcription.Accordingly, it was rationalized that a purified ˜1,000 base pairsection of chromatin at the 5′ end of the GAL1 gene from cells grown ingalactose would contain histone PTMs correlated with activetranscription and cellular machinery necessary for transcription, whilethe same chromatin section from cells grown in glucose would be enrichedwith histone PTMs associated with transcriptional repression. Priorpublications have documented that H3 acetylation is enriched on the 5′end of the active galactose-induced GAL1 gene, while in the presence ofglucose it contains H3K36me3 (Shukla et al., 2006; Houseley et al.,2008). Results presented in the Examples herein with ChAP-MS, supporteach of these prior findings (FIG. 5). Furthermore, the presence ofdoubly acetylated histones (H3K9acK14ac, H3K18acK23ac, H4K5acK8ac,H4K12acK16ac) during transcriptional activation was identified. Thisdemonstrates how ChAP-MS may be used to study the combinatorial “code”of histone modifications at given chromosome regions without the needfor prior identification of PTMs, PTM-specific antibodies, or sequentialchromatin put-downs. Considering H4K12acK16ac for example, theidentification of the double acetylation is unique to the ChAP-MSapproach as antibodies to this double acetylation do not exist, thus onecould not have performed a biased ChIP analysis. Additionally, it hasbeen reported that commercially available antibodies to singleacetylation at H4K12 or H4K16 are cross-reactive with other H4acetylations and that double acetylation of H4K12K16 significantlyalters the specificity of the antibody to the singly acetylated sites(Bock et al., 2011)—a limitation specific to antibodies used in biasedChIP studies and not to the unbiased ChAP-MS approach that usesquantitative mass spectrometric readout. The ChAP-MS approachsimultaneously identified the presence of RNA polymerase (Rpb1, Rpb2)and FACT component Spt16 (which aids in reorganizing chromatin for RNApol activity) under these transcriptionally active conditions. Also ofinterest was the identification of Gal3 at actively transcribing GAL1,which has previously been shown to inhibit the repressive activity ofGal80 at the GAL10/GAL1 locus (Platt and Reece, 1998). It wasdemonstrated how the ChAP-MS approach may be utilized to study chromatindynamics at GAL1 under different states of gene transcription. Ofparticular interest for future functional studies may be the upstreamactivating sequence which binds the Gal4 actuator and Gal80 repressorwhich may allow better understand of the events surrounding the switchfrom repression to activation at GAL1 and GAL10, as well as the middleand 3′ end of GAL1 to understand the processes of elongation andtermination, respectively.

Utility of ChAP-IVIS as a General Tool for Studying Chromatin Biology

The ChAP-MS technology presented here demonstrates the ability to purifya unique chromosome section on the order of four to five nucleosomes inlength from an in vivo source that can subsequently be subjected tosensitive proteomic studies. ChAP-MS has numerous advantages relative totraditional ChIP, including the ability to unbiasedly detectproteins/PTMs at a specific genomic locus and the identification ofcombinatorial histone modifications on a single histone molecule.Furthermore, ChAP-MS only requires approximately an order of magnitudemore cells relative to biased ChIP studies, which is a huge advantage ifdoing more than ten blind ChIP studies at a given region is factored in(chances are many antibodies for many proteins would be heavily investedin, trying to guess a specifically bound protein/PTM). In this regard,ChAP-MS is a more cost-effective option for characterizing specificallybound proteins and histone PTMs relative to ChIP. Future derivations ofthis technology may employ targeted mass spectrometric approaches forbetter determination of combinatorial histone PTMs as well asidentification of other regulatory PTMs on nonhistone proteins fromthese isolated sections (Taverna et al., 2007). Given the sensitivity ofthe mass spectrometry analysis employed and the relatively modestbiological starting material, the findings presented in the Examplesherein also establish a framework for applying ChAP-MS to profile acrossentire regions of chromosomes or investigate higher eukaryotic systems.Regardless, any advances that permit ChAP-MS analysis of in vivountagged or unaltered samples, like tissues, will undoubtedly havevaluable applications for investigating altered gene transcriptionmechanisms in human disease states, as this technique could provide acomprehensive way to intelligently identify targets for therapeutics.

Experimental Procedures for Examples 1-3 Construction of the LEXA::GAL1pLexA-PrA Strain

The LEXA::GAL1 pLexA-PrA strain used to affinity enrich GAL1 chromatinwas designed to have a LexA DNA binding site just upstream of the GAL1start codon and contains a plasmid constitutively expressing a LexA-PrAfusion protein. In S. cerevisiae from the W303a background, the GAL1gene was genomically replaced with URA3 using homologous recombination.Next, the GAL1 gene (+50 base pairs up- and downstream) was PCRamplified with primers that incorporated a LexA DNA binding site(5′-CACTTGATACTGTATGAGCATACAGTATAATTGC) immediately upstream of the GAL1start codon. This LEXA::GAL1 cassette was transformed into thegal1::URA3 strain and selected for growth with 5-fluoroorotic acid,which is lethal in URA3 expressing cells. Positive transformants weresequenced to ensure homologous recombination of the cassette to createthe LEXA::GAL1 strain. A plasmid that constitutively expresses LexA-PrAfusion protein with TRP selection was created by amplification of thePrA sequence from template pOM60 via PCR and subcloning into theSacI/SmaI ends of the expression plasmid pLexA-C. Transforming thisplasmid into the LEXA:GAL1 strain gave rise to the LEXA:GAL1 pLexA-PrAstrain. Additionally, a control used in these studies was W303a S.cerevisiae transformed only with pLexA-PrA.

Cell Culture

Strains LEXA:GAL1 pLexA-PrA and pLexA-PrA were grown in yeast syntheticmedia lacking tryptophan to mid-log phase at 30° C. LEXA:GAL1 pLexA-PrAstrain growths were done with isotopically light lysine, while strainpLexA-PrA was cultured exclusively with isotopically heavy¹³C6¹⁵N₂-lysine. For each strain, 12 l of media containing either 2%glucose or 3% galactose were grown to yield ˜5×10¹¹ cells per growthcondition. At mid-log phase, the cultures were crosslinked with 1.25%formaldehyde for 5 min at room temperature and then quenched with 125 mMglycine for 5 min at room temperature. Cells were harvested bycentrifugation (2,500×g) and frozen in liquid nitrogen as pellets insuspension with 20 mM HEPES (pH 7.4), 1.2% polyvinylpyrrolidone (1 ml/10g of cell pellet). Frozen cell pellets were mixed as follows at 1:1 cellweight ratios: (1) LEXA:GAL1 pLexA-PrA isotopically light in glucoseplus pLexA-PrA isotopically heavy control in glucose (2) LEXA:GAL1pLexA-PrA isotopically light in galactose plus pLexA-PrA isotopicallyheavy control in galactose. Cell mixtures were cryogenically lysed underliquid nitrogen temperature with a Retsch MM301 ball mill (Smart et al.,2009; Tackett et al., 2005a).

ChAP-MS Procedure

Each of the following two cell lysates were processed for purificationof GAL1 chromatin: (1) LEXA:GAL1 pLexA-PrA isotopically light in glucoseplus pLexA-PrA isotopically heavy control in glucose, referred to as theglucose ChAP-MS, and (2) LEXA:GAL1 pLexA-PrA isotopically light ingalactose plus pLexA-PrA isotopically heavy control in galactose,referred to as the galactose ChAP-MS. Twenty grams of frozen cell lysate(˜5×10¹¹ cells) was used for each of the glucose and galactose ChAP-MSanalyses. ChAP-MS steps were performed at 4° C. unless otherwise noted.Lysates were resuspended in 20 mM HEPES (pH 7.4), 1 M NaCl, 2 mM MgCl₂,1 M urea, 0.1% Tween 20, and 1% Sigma fungal protease inhibitor cocktailwith 5 ml buffer per gram of frozen lysate. Lysates were subjected tosonication with a Diagenode Bioruptor UCD-200 (low setting, 30 s on/offcycle, 12 min total time) in 20 ml aliquots to yield ˜1 kb chromatinfragments. Supernatants from sonicated lysates were collected bycentrifugation at 2,000×g for 10 min. Dynabeads (80 mg) coated withrabbit IgG were added to the lysates and incubated for 4 hr withconstant agitation (Byrum et al., 2012a). Dynabeads were collected witha magnet and washed 5 times with the purification buffer listed aboveand 3 times with 20 mM HEPES (pH 7.4), 2 mM MgCl₂, 10 mM NaCl, 0.1%Tween 20. Washed Dynabeads were treated with 0.5 N ammoniumhydroxide/0.5 mM EDTA for 5 min at room temperature to elute proteins.Eluants were lyophilized with a Savant SpeedVac Concentrator.Lyophilized proteins were resuspended in Laemmli SDS-PAGE loadingbuffer, heated to 95° C. for 20 min, resolved with 4%-20% tris-glycineInvitrogen precast gels, and visualized by colloidal Coomassie staining.

High-Resolution Mass Spectrometry and Data Analysis

Gel lanes were sliced into 2 mm sections and subjected to in-gel trypsindigestion (Byrum et al., 2011a, Byrum et al., 2011b, Byrum et al.,2012a; Tackett et al., 2005b). Peptides were analyzed with a ThermoVelos Orbitrap mass spectrometer coupled to a Waters nanoACQUITY liquidchromatography system (Byrum et al., 2011b). Using a data-dependentmode, the most abundant 15 peaks were selected for MS² from ahigh-resolution MS scan. Proteins were identified and the ratio ofisotopically light/heavy lysine-containing tryptic peptide intensity wasdetermined with Mascot and Mascot Distiller. The search parametersincluded: precursor ion tolerance 10 ppm, fragment ion tolerance 0.65Da, fixed modification of carbamidomethyl on cysteine, variablemodification of oxidation on methionine, and two missed cleavagespossible with trypsin. A threshold of 95% confidence for proteinidentification, 50% confidence for peptide identification and at leasttwo identified peptides per protein was used, which gave a 2% peptidefalse discovery rate. All specifically associating proteinidentifications and ratios were manually validated.

A baseline was established for nonspecifically associated proteins withnonspecifically enriched ribosomal proteins (Smart et al., 2009). Theaverage percent isotopically light peptides from 20 ribosomal proteinsfrom the glucose and galactose growth condition were used to establishthis nonspecifically associated baseline. This resulted in anonspecifically associated baseline of 49.93%±2.12% light for theglucose ChAP-MS and 66.8%±7.1% light for the galactose CHAP-MS. Proteinswere categorized as specifically associating if the percent light wasgreater than 2 SDs above the ribosomal level (Tables 4 and 5) (Smart etal., 2009). Duplicate ChAP-MS procedures showed Pearson and Spearmancorrelation coefficient p values of <0.001.

ChIP and Gene Transcription Assays

ChIP and gene transcription assays were performed as previously reported(Tackett et al., 2005b; Taverna et al., 2006). Assays were performed intriplicate and analyzed by real time PCR.

Introduction for Examples 4-5

One of the most compositionally diverse structures in a eukaryotic cellis a chromosome. A multitude of macromolecular protein interactions andepigenetic modifications must properly occur on chromatin to drivefunctional aspects of chromosome biology like gene transcription, DNAreplication, recombination, repair and sister chromatid segregation.Analyzing how proteins interact in vivo with chromatin to direct theseactivities and how epigenetics factors into these mechanisms remains asignificant challenge owing to the lack of technologies tocomprehensively analyze protein associations and epigenetics at specificnative chromosome sites. Chromatin immunoprecipitation (ChIP) assayshave traditionally been used to better understand genome-widedistributions of chromatin-associated proteins and histonepost-translational modifications (PTMs) at the nucleosome level (Cermaket al., 2011). However, major drawbacks of current ChIP-based methodsinclude their confinement to examining singular histone PTMs or proteinsrather than simultaneous profiling of multiple targets, the inability ofChIP to directly determine the co-occupancy of particular histone PTMsand that ChIP is reliant on the previous identification and developmentof affinity reagents against the molecular target. A more comprehensiveand unbiased approach would be the biochemical isolation of a specificnative genomic locus for proteomic identification of proteins-associatedand histone PTMs. Similar approaches have been performed for largestructures like telomeres, engineered plasmids or engineered loci(Griesenbeck et al., 2003; Dejardin and Kingston, 2009; Hoshino andFuji, 2009; Akiyoshi et al., 2009; Unnikrishnan et al., 2010; Byrum etal., 2012b); however, the proteomic analysis of a small native genomicregion without genomic engineering has yet to be performed. To worktoward proteomic studies of native chromatin regions (i.e. sections ofchromatin that are unaltered genetically and spatially the genome), werecently developed a technique termed Chromatin Affinity Purificationwith Mass Spectrometry (ChAP-MS) that provides for the enrichment of anative 1-kb section of a chromosome for site-specific identification ofprotein interactions and associated histone PTMs (Byrum et al., 2012b).This ChAP-MS approach uses the association of an ectopically expressedaffinity-tagged LexA protein with a genomically incorporated LexA DNAbinding site for site-specific chromatin enrichment. The ChAP-MSapproach provides for the isolation of chromatin from the native site inthe chromosome; however, one must genomically engineer a LexA DNAbinding site, which could alter the native state of the chromatin andwhich requires a biological system readily amendable to genomicengineering.

To alleviate genomic engineering for affinity enrichment of chromatinsections, we report the use of modified transcription activator-like(TAL) effector proteins to site-specifically target a native section ofa chromosome for purification and proteomic analysis. We term thisapproach TAL-ChAP-MS (FIG. 7A). TAL effector proteins are fromXanthomonas, which infects plants and translocates TAL effectors intocells where they serve as transcription activators (Scholze and Boch,2010; Scholze and Boch, 2011; Doyle et al., 2012). TALs contain acentral domain of 18 tandem repeats of 34 amino acids each, which directsequence-specific DNA binding (Doyle et al., 2012; Cermak et al., 2011).Binding to a given nucleobase in DNA is determined by two adjacent aminoacids (12 and 13) within each of the 18 repeats (Scholze and Boch,2010). Thus, by mutating these amino acids in each of the 18 tandemrepeats, one can ‘program’ binding to a given 18-nt region of DNA invivo. TAL proteins have been validated in cell culture for targetingnucleases for genome editing and for targeting transcription activators(Miller et al., 2011; Geissler et al., 2011). To test the ability of aTAL protein to serve as an affinity enrichment reagent for nativechromatin isolation, a TAL protein was designed that bound a unique18-nt region of DNA in the promoter region of the GAL1 gene inSaccharomyces cerevisiae (FIG. 7B). We chose to analyze proteins andhistone PTMs regulating the galactose-induced gene transcription of GAL1because (1) this is a well-studied genomic locus, which will provide forproof-of-principle analysis, and (2) we previously used this locus todevelop the ChAP-MS technique (Byrum et al., 2012b); thus, a comparisoncan be made to the new TAL-ChAP-MS approach.

One of the major complications for studying specific proteinassociations with purified protein complexes or with chromatin is theco-enrichment of non-specifically associating proteins. Thisparticularly becomes an issue when studying low copy number entitiessuch as a single genomic locus. With the advancement of high-resolutionand sensitive mass spectrometry in recent years, it has been suggestedthat >10⁹ cell equivalents are needed to study single genomic loci withproteomic approaches (Chait, 2011). In agreement, our ChAP-MS studiesused 10¹¹ cells for isolation of GAL1 promoter chromatin at levelssufficient for proteomic analysis (Byrum et al., 2012b). When scaling uppurifications of low copy entities to meet the sensitivity necessary forhigh-resolution mass spectrometric analysis, the issue of co-purifyingabundant non-specific proteins becomes a major challenge. In the ChAP-MSapproach (Byrum et al., 2012b), we used an isotope-labeling strategy tocategorize whether a protein co-enriching with a section of chromatinwas specifically associated or a contaminant. Limitations forisotope-labeling approaches are cost and having biological systems ofstudy that are amendable to stable isotope-labeling with amino acids. Tocircumvent the use of isotope-labeling, we now have incorporatedlabel-free quantitative mass spectrometry in the TAL-ChAP-MS workflow.The described TAL-ChAP-MS approach can therefore provide for thepurification of a native chromatin region for label-free quantitativeproteomic analysis, which will greatly simplify studies of how proteinsand combinatorial histone PTMs regulate chromosome metabolism.

Example 4 Development of TAL-ChAP-MS

A schematic of the TAL-ChAP-MS approach to purify native chromatin forproteomic analysis is shown in FIG. 7A. To demonstrate the utility ofthe TAL-ChAP-MS approach, we used a TAL protein to target the promoterchromatin region upstream of the galactose-inducible GAL1 gene in S.cerevisiae (FIG. 7B). Yeast cells were grown in the presence ofgalactose to induce transcription of the GAL1 gene, which will recruitproteins and histone PTMs that activate transcription. A wild-typeculture and a culture of cells containing a plasmid that expressed aPrA-tagged TAL protein that bound the GAL1 promoter region were grownand subjected to in vivo formaldehyde cross-linking to preservechromatin structure during purification (Byrum et al., 2011a; Byrum etal., 2011b). Following cryogenic cell lysis and sonication of chromatinsections to ˜1 kb, each lysate was independently subjected to affinityenrichment of PrA with IgG-coated Dynabeads. Proteins co-enriching withTAL-PrA from the cells containing the pTAL-PrA plasmid and thoseenriching as contamination from the control cells with no plasmid wereidentified by high-resolution mass spectrometry. Using label-freequantitative analyses, the relative enrichment of proteins and histonePTMs specifically hound to the GAL1 promoter chromatin were identified.

Saccharomyces cerevisiae cells were transformed with pTAL-PrA, andprotein expression was validated by western blotting (FIG. 7C). Toevaluate whether TAL-PrA expression affected galactose-inducedtranscription of GAL1, cDNA was prepared from wild-type and wild-type(+pTAL-PrA) cells under glucose (transcriptionally repressed GAL1) andgalactose (transcriptionally active GAL1) growth conditions.Quantitative rtPCR of this cDNA revealed that expression of TAL-PrA didnot affect galactose-induced GAL1 transcription (FIG. 7D). To determinewhether TAL-PrA enriched chromatin at the GAL1 promoter region, ChIP wasperformed to the PrA-tag in cells from glucose and galactose growths(FIG. 7E-G). Under transcriptionally active conditions, TAL-PrAspecifically enriched chromatin from the GAL1 promoter region relativeto sequences 2 kb up- and downstream (FIG. 7F). The level of chromatinenrichment by TAL-PrA under transcriptionally active conditions wassimilar to the level used for proteomic studies with LexA-PrA affinityenrichment in the ChAP-MS approach (Byrum et al., 2012b). Interestingly,the TAL-PrA protein did not show enrichment of the GAL1 promoterchromatin under transcriptionally repressive glucose growth conditions(FIG. 7G). One possibility of many is that the lack of enrichment couldbe due to inaccessibility of the TAL-PrA to the genomic target due toaltered chromatin structure under transcriptionally repressiveconditions—highlighting the importance for measuring specific chromatinenrichment of the TAL protein before using this approach for specificchromatin enrichment. In the previous publication of the ChAP approach(Byrum et al., 2012b), a LexA-PrA was targeted just upstream of thestart codon of GAL1 for enrichment of chromatin, which showed enrichmentunder both glucose and galactose growth conditions. Importantly, the TALused in the current study was targeted 193 bp upstream of the targetsite of LexA, which suggests that proximal regions may be differentiallyaccessible to DNA-binding affinity reagents under varioustranscriptional states. In addition to analyzing enrichment of GAL1chromatin relative to proximal sequences (FIG. 7E-G), enrichment of GAL1chromatin was measured relative to the five most homologous sequences inthe genome (Table 6). The GAL1 target DNA showed 4.6-fold betterenrichment relative to the next five most similar sites in thegenome—demonstrating specificity of the TAL protein used in this studyto the targeted sequence at the GAL1 promoter region. Collectively, thedata in FIG. 7C-G and Table 6 demonstrate that the TAL-ChAP-MS approachcan provide enriched chromatin from the GAL1 promoter undertranscriptionally active conditions that would be suitable for proteomicstudies.

Example 5 Using TAL-ChAP-MS to Identify Proteins and Histone PTMs at theGAL1 Promoter

As detailed in the Experimental Procedures for Examples 4-5 section,chromatin from the transcriptionally active GAL1 promoter was enrichedwith TAL-PrA and resolved by SDS-PAGE (FIG. 8A). The similarCoomassie-stained protein pattern for the TAL-PrA and wild-type controlsamples in FIG. 8A demonstrates that the co-enrichment of contaminatingproteins was a major issue for this approach. Accordingly, thelabel-free spectral counting approach described in the ExperimentalProcedures for Examples 4-5 section was used to identify proteinsspecifically enriched with the TAL-PrA. High-resolution massspectrometry coupled with label-free proteomics was used to identifyproteins and histone PTMs specifically enriched with the GAL1 promoterchromatin (FIG. 8B and Table 7). We focused our analysis on the top 10%of enriched proteins (54 proteins) that each showed >15-fold enrichmentwith the TAL-PrA (Table 7). Four of these 54 proteins (Rpb1, Rpb2, Spt16and Gal3) are involved with active transcription of GAL1, and these arethe same four proteins previously identified at the promoter of GAL1with the ChAP-MS approach (Byrum et al., 2012b). Rpb1 and Rpb2 are RNApolymerise components, and Spt16 is a subunit of yFACT that aids inre-organizing chromatin for RNA polymerase activity. Gal3 has previouslybeen shown to inhibit the repressive activity of Gal80 at GAL1 locus(Platt and Reece, 1998). Rpb1, Rpb2, Spt16 and Gal3 were confirmed to beassociated adjacent to the TAL-PrA genomic binding site with standardChIP (FIG. 8C). Thus, the TAL-ChAP-MS approach identified precisely thesame proteins as the published ChAP-MS approach during transcriptionalactivation at the promoter of GAL1, thereby validating the TAL-ChAP-MSapproach for studying the local proteome of small chromatin regions andthe use of label-free proteomic approaches for quantifying suchenrichments. Many of the other 50 proteins identified as >15-foldenriched with TAL-PrA are typical non-specific protein associationsfound in affinity purifications (e.g. highly abundant metabolic andribosomal proteins).

In addition to protein associations with the GAL1 promoter, thefollowing single histone PTMs were identified under transcriptionallyactive conditions: H3K14ac, H3K56ac, H3K79me1/me2/me3, H2BK I7ac andH2AK7ac; and the following combinatorial histone PTMs: H3K9acK14ac,H3K18acK23ac, H2BK6acK11ac and H2BK11acK17ac (FIG. 8B and Table 8). Thepresence of H3K14ac was confirmed by standard ChIP (FIG. 8C). Previouslyusing ChAP-MS and routine ChIPs (Byrum et al., 2012b), a similar profileof singly acetylated H3 lysine residues was identified at the GAL1promoter region, thus confirming the utility of the TAL-ChAP-MSapproach. In addition to the acetylations observed in the ChAP-MS study,the TAL-ChAP-MS approach additionally identified methylation of H3K79.As previously reported for the ChAP-MS approach, the TAL-ChAP-MSapproach uncovered combinatorial sets (i.e. multiple PTMs on singlepeptides) of histone PTMs under transcriptionally active conditions atthe promoter of GAL1. The use of a technology like TAL-ChAP-MS toidentify previously unknown combinatorial modifications is crucial tounderstand the epigenome, as specific antibodies to combinatorialhistone PTMs are not usually available for standard approaches likeChIP. In general terms, acetylation of histone lysine residues andmethylation of H3K79 correlate to transcriptional activation(Kouzarides, 2007); thus, the histone PTMs uncovered by TAL-ChAP-MScorrelate to the active transcription state of GAL1 in the presence ofgalactose.

Discussion for Examples 4-5

We describe a novel approach called TAL-ChAP-MS that provides for thebiochemical isolation of 1-kb native chromatin sections for proteomicidentification of specifically associated proteins and combinatorialhistone PTMs. The described TAL-ChAP-MS approach overcomes limitationsof the ChAP-MS approach (Byrum et al., 2012b), as genomic engineering isnot necessary for TAL-based affinity enrichment and because proteinenrichment with a given locus can now be determined with label-freeproteomics. Even without genomic engineering of the DNA, the ChAP-MSapproach does require targeting of a DNA-binding affinity enrichmentreagent (i.e. the TAL protein), which has the potential to perturb thechromatin state. However, the data in FIG. 7D demonstrate thattranscription of GAL1 is not altered on TAL targeting, which supportsmaintenance of the chromatin integrity for the studies reported here.Targeting TALs to different sequences in adjacent genomic regions thatwould provide for purification of overlapping chromatin sections is onepossible way for investigators to overcome concerns of TAL binding (i.e.a tiling approach). The implications of the TAL-ChAP-MS approach arefar-reaching as investigators can now begin to elucidate the dynamics ofchromatin regulation in a site-specific and comprehensive manner.Researchers will now only need to ‘reprogram’ the DNA-bindingspecificity of the TAL protein to obtain a unique affinity purificationreagent for their chromosome region of interest. Using the TAL-ChAP-MSapproach brings researchers closer to being able to take molecular‘snapshots’ of the assembly and disassembly of proteins on chromatin andhow epigenetic states are modulated at small genomic loci.

Experimental Procedures for Examples 4-5 pTAL-PrA Plasmid, Real-TimertPCR and ChIP

For affinity enrichment of chromatin from the promoter region of theGAL1 gene in S. cerevisiae, a TAL protein was designed (by the GeneArtPrecision TAL services of Life Technologies) to bind a unique 18-ntsequence (GGGGTAATTAATCAGCGA) 193 base pairs upstream of the GAL1open-reading frame (FIG. 7B). The TAL protein was designed as atruncation that lacked the native N-terminal transcription activationdomain, but it contained the site-specific DNA-binding region. Todevelop an affinity enrichment reagent, the LexA-coding region ofpLexA-PrA [plasmid that constitutively expresses a PrA-tagged LexAprotein under TRP selection; from (Byrum et al., 2012b)] was replacedwith the TAL-coding region to generate pTAL-PrA. Real-time qPCRmeasurement of galactose-induced transcription of GAL1 and all ChIPstudies were performed as reported in (Byrum et al., 2012b).

TAL-ChAP-MS

To test the TAL-ChAP-MS approach at the promoter region of GAL1,wild-type and wild-type (+pTAL-PrA) S. cerevisiae (W303 matA) cells werecultured to mid-log phase in 3% galactose-containing media, subjected to1.25% formaldehyde cross-linking, cryogenically lysed and subjected tosonication to shear genomic DNA to ˜1 kb [as detailed in (Byrum et al.,2012b; Byrum et al., 2011a; Byrum et al., 2011b)]. Immunoglobulin G(IgG)-coated Dynabeads were added to lyste from ˜10¹¹ cells from eachgrowth separately [as detailed in (Byrum et al., 2012b)]. Proteinsco-enriching with the TAL-PrA (wild-type cells +pTAL-PrA lysate) orproteins non-specifically binding to the Dynabeads (wild-type celllysate) were resolved by SDS-PAGE/Coomassie-staining (FIG. 8A), excisedas 2-mm bands from the entire gel lane, digested in-gel with trypsin andsubjected to high-resolution tandem mass spectrometric analysis with aThermo Velos Orbitap mass spectrometer [as reported in (Byrum et al.,2012b)]. Proteins and typical histone PTMs (lysine acetylation andmethylation) were identified using Mascot (Tables 7 and 8). To measureenrichment of a protein, the normalized spectral abundance factor(Zybailov et al., 2006) was calculated for each protein in each lane bydividing the number of spectral counts (normalized for the size of theprotein) of a given protein by the sum of all normalized spectral countsof all proteins in the gel lane (Byrum et al., 2011c). The enrichmentlevel for each protein was identified by calculating the fold enrichment(TAL-PrA/wild type) using the normalized spectral abundance factorvalues (Table 7). Proteins with a fold enrichment >2 (511 of 1459proteins identified) were used to generate a quantile plot of foldenrichment with GAL1 promoter chromatin (FIG. 8B).

Introduction for Example 6

For the work presented, a “local epiproteome” refers to not only thehistone PTMs at a specific chromosomal location that are involved in aparticular activity (Dai and Rasmussen, 2007), but also to the otherproteins associated with the region in addition to the histones.Identifying the components of a specific epiproteome can provideunprecedented insight into the molecular and epigenetic mechanismsregulating an activity. For example, gene transcription could havevarious epiproteomes that regulate initiation, elongation andtermination. A recently realized milestone for measuring localepiproteomes has been the development of affinity enrichment proceduresto isolate small regions of chromatin (Byrum et al., 2013; Byrum et al.,2012b; Dejardin and Kingston, 2009; Akiyoshi et al., 2009; Hoshino andFujii, 2009; Griesenbeck et al., 2003; Unnikrishnan et al., 2010;Hamperl et al., 2014). Purification of a small region of chromatin fromthe cellular milieu is one of the most challenging aspects of theseapproaches as the proteins and histone PTMs specifically isolated withthe targeted chromatin typically constitute a small fraction of theidentified proteins—most of which are non-specific associations (Byrumet al., 2013; Byrum et al., 2012b; Byrum et al., 2011a). We developedtwo approaches using quantitative high resolution mass spectrometry thatdistinguish whether proteins and histone PTMs identified duringepiproteome measurements are “specific” to the target chromatin or are“non-specific” contaminants (Byrum et al., 2013; Byrum et al., 2012b).These quantitative approaches are critical components of our ChAP-MS(Chromatin Affinity Purification with Mass Spectrometry) platform oftechnologies that enable local epiproteome analysis. Included in thisplatform are the first generation ChAP-MS and second generationTAL-ChAP-MS approaches (Byrum et al., 2013; Byrum et al., 2012b). TheChAP-MS approach, which used a targeted LexA protein as an affinityreagent, demonstrated the first unambiguous epiproteome measurement. TheTAL-ChAP-MS approach achieved similar high resolution and specificity byusing the genomic targeting ability of the TALEN (TranscriptionActivator-Like Effector Nuclease) system for local epiproteome isolationand analysis (Byrum et al., 2012b; Scholze and Boch, 2011).

Described here is the third generation technology termed CRISPR-ChAP-MS(FIG. 9). The prokaryotic viral defense system CRISPR (ClusteredRegularly Interspaced Palindromic Repeats) has recently been developedas a genome-editing tool for eukaryotes (Mali et al., 2013). The corecomponents of this system include the Cas9 nuclease, which is able tocreate double-strand breaks in DNA, and guide RNA (gRNA), which is boundby Cas9 and serves to direct this complex to a target sequencecomplementary to the gRNA. Using the Type II CRISPR system from S.pyogenes, we have harnessed the specific gene-targeting capability ofthe Cas9/gRNA complex to isolate and unambiguously identify a specificlocal epiproteome. We created a PrA-tagged version of Cas9 with acatalytically inactive nuclease along with a gRNA to target the promoterregion of the GAL1 gene in S. cerevisiae to validate the CRISPR-ChAP-MStechnology (FIG. 9).

To isolate the targeted chromatin, cells were treated with formaldehydeto stabilize interactions (Byrum et al., 2012b), chromatin was shearedto fragments approximately 1 kb in length, and the target chromatin wasaffinity purified using the PrA tag. Affinity tagged versions of Cas9have been shown to target chromatin for partial enrichment (Fujita andFujii, 2013); however, a quantitative analysis of the specifically boundproteins and histone PTMs has not been reported. Here using ourCRISPR-ChAP-MS approach that does provide for quantitativeidentification of specifically bound proteins and histone PTMs, the GAL1promoter chromatin from yeast was isolated under transcriptionallyactive conditions and subjected to a label-free quantitative massspectrometric workflow to identify the specific components of the localepiproteome. Relative to the first and second generations of the ChAP-MStechnological platform, CRISPR-ChAP-MS shows an enhanced ability toisolate targeted chromatin, which is critical for epiproteome analysis.The TAL-based approach also requires design of a specific TAL proteinfor each sequence targeted whereas CRISPR-ChAP-MS only requiressite-directed mutagenesis to alter the gRNA for genomic targeting, whichprovides a more cost effective approach that can easily be multiplexedto target additional sites.

Example 6 A CRISPR-Based Approach for High Resolution EpiproteomeIdentification

To validate the CRISPR-ChAP-MS approach, the promoter chromatin of theGAL1 gene was targeted for enrichment in S. cerevisiae. This region ofchromatin is an attractive target for validation studies as one cansupply yeast with galactose in place of glucose to rapidly andsynchronously stimulate transcriptional activation of GAL1—therebysetting a transcriptionally active chromatin state for epiproteomeanalysis. Cells were transformed with plasmids expressing a nucleaseinactive and PrA-tagged version of Cas9 (pPrA-Cas9) and/or expressinggRNA specific to the promoter region of the GAL1 gene (pgRNA-GAL1).Similar expression of PrA-Cas9 in glucose and galactose was demonstratedby Western-blotting (FIG. 10A). To evaluate whether expression of thisPrA-Cas9/gRNA complex affected transcription of GAL1, cDNA was preparedfrom cells in glucose (transcriptionally repressed GAL1) and galactose(transcriptionally active GAL1) and was analyzed by quantitativereal-time PCR. GAL1 transcription was similar in cells expressingPrA-Cas9/gRNA compared to cells expressing only PrA-Cas9, indicatingthat expression of PrA-Cas9/gRNA does not drastically altertranscriptional activation (FIG. 10B). To determine whether thisexpressed PrA-Cas9/gRNA complex was bound to and could enrich chromatinat the GAL1 promoter region, ChIP was performed to PrA-Cas9 in cellsfrom glucose and galactose cultures. GAL1 promoter chromatin wasenriched in a gRNA dependent manner with PrA-Cas9 from both glucose(4.9-fold) and galactose (70-fold) growth conditions (FIG. 10C). Regions2 kb up- or downstream did not show enrichment (FIG. 10C), demonstratingthat chromatin purification was localized to the gRNA target region. Inprevious studies using TAL proteins targeted to the same chromatinregion (Byrum et al., 2013), a ˜6-fold enrichment was observed undergalactose growth conditions and no enrichment under glucose growth.Therefore, the enrichment observed with PrA-Cas9/gRNA ingalactose-containing media is greater than an order of magnitude higherrelative to a TAL targeted to this region of chromatin.

To determine if enrichment using CRISPR-ChAP was specific, a series ofpotential off-target sites were analyzed (FIG. 10C). The four mostsimilar sites in the genome to the first 12 base-pairs of the 20base-pairs targeted at GAL1 by gRNA-GAL1 were analyzed by qPCR-ChIP forPrA-Cas9/gRNA binding. The first 12 base-pairs of the 20 base-pairtarget sequence strongly influence gRNA-directed binding specificity (Fuet al., 2013). The off-target (OT) sites contained 14/20 (OT1), 15/20(OT2), 15/20 (OT3) and 13/20 (OT4) of sequence identity relative to theGAL1 target DNA. Two of the four off-target sites showed 3.2- and4.4-fold (OT1 & OT2) enrichment with PrA-Cas9/gRNA (FIG. 10C). For mosteffective targeting of Cas9 to a genomic region, the 20 base-pair targetregion needs to contain a protospacer-activation motif (PAM motif)immediately 3′ to the target DNA. In the type II S. pyogenes system usedin this work, the PAM motif is NGG (Mali et al., 2013; DiCarlo et al.,2013). Accordingly, OT1 and OT2 that showed Cas9/gRNA enrichmentcontained a PAM motif, while OT3 and OT4 did not. This demonstrated thatoff-target binding of the PrA-Cas9/gRNA complex targeting GAL1 isenhanced with a PAM motif and can provide ˜4-fold off-target enrichment.This ˜4-fold off-target enrichment is much lower than the 70-foldenrichment observed for transcriptionally active GAL1 promoter chromatinand will not complicate large scale proteomic approaches as thespecifically bound proteins/PTMs will dominate the mass spectrometricdata collection. The enrichment of GAL1 promoter chromatin under glucosegrowth conditions was 4.9-fold whereas off-target binding can contributeup to ˜4-fold enrichments. Therefore, purification of GAL1 promoterchromatin under glucose growth conditions was not pursued for largescale proteomic analysis, but rather the 70-fold enriched chromatin fromgalactose growth conditions was used for subsequent proteomic studies.The Cas9/gRNA and previously reported TAL results illustrate thatDNA-binding affinity reagents may differentially access chromatin indifferent states; thus, care has to be taken to test for specificenrichment prior to proteomic studies (Byrum et al., 2013). As theCRISPR-based approaches become more engineered for DNA-bindingspecificity, off-target issues will have less impact on theCRISPR-ChAP-MS approach (Jiang et al., 2013).

To demonstrate the utility of the CRISPR-ChAP-MS approach, the GAL1promoter chromatin was enriched from 1×10¹⁰ cells that were grown inmedia containing galactose. As a control for quantitative massspectrometric identification of proteins as “specific” or “non-specific”to the purification, CRISPR-ChAP-MS was performed with PrA-Cas9expressing cells either with or without gRNA-GAL1. Of particularimportance for purification of small regions of chromatin, anexperimentally-determined amount of formaldehyde cross-linking andsonication must be used to ensure that a native chromatin region can beisolated and analyzed (Byrum et al., 2013; Byrum et al., 2012b; Byrum etal., 2011a). Cells were cross-linked with 1.25% formaldehyde, lysedunder cryogenic conditions with a ball mill, and after thawing weresonicated in purification buffer to yield chromatin fragments ˜1 kb inlength. Dynabeads coated with IgG were used to affinity purify thePrA-Cas9/g RNA complex or control PrA-Cas9 with any associated proteinsand posttranslationally modified histones. Isolated proteins wereresolved by SDS-PAGE (FIG. 11A), excised from the entire gel lane in 2mm bands and subjected to in-gel trypsin digestion. Tryptic peptideswere analyzed by high resolution mass spectrometry with a Thermo VelosOrbitrap mass spectrometer as reported (Byrum et al., 2013). Proteinsand histone PTMs (acetylation and mono-, di- and trimethylation oflysine) were identified with Mascot (Tables 9 & 10).

To determine which proteins were specifically enriched with the GAL1promoter chromatin, a quantitative mass spectrometric approach was usedto compare proteins identified with PrA-Cas9/gRNA and PrA-Cas9 alone.This reported approach uses normalized spectral abundance factors torepresent the relative level of each protein in each sample, which canthen be cross-compared to identify those proteins/PTMs enriched withPrA-Cas9/g RNA (Byrum et al., 2013; Zybailov et al., 2006; Byrum et al.,2013b). Using this approach, 86 out of 1832 identified proteins werefound to enrich with PrA-Cas9/g RNA (Table 9). 11 of the 86 proteinswere related to transcription (RebI, SptS, Toa2, BafI, Sin3, H2B2, Ume1,Pob3, Rsc6, Rpa14, Rsc7), while the other 75 were common contaminantsfound in affinity enrichments (Byrum et al., 2013; Byrum et al. 2012b).In addition to proteins, acetylation of lysine 14 on histone H3 (H3K14)and H3K23 were found enriched with the GAL1 promoter chromatin (Table10). Both H3K14ac and H3K23ac are correlated to active transcriptionalstates of chromatin. ChIP for a subset of these proteins/PTMs (SptS,Pob3, Rsc6, Rsc7 and H3K14ac) was used to verify that theseproteins/PTMs are components of the epiproteome at the targeted regionof GAL1 promoter chromatin (FIG. 11B). H3K14ac was identified at theGAL1 promoter region with our first and second generation ChAPtechnologies (Byrum et al., 2013; Byrum et al. 2012b), while Pob3, SptS,Rsc6 and Rsc7 are unique to this study. Pob3 forms a complex with Spt16to make yFACT, which promotes chromatin rearrangement to allowprogression of RNA polymerase. Spt16 was identified with our first andsecond generation ChAP technologies at GAL1 (Byrum et al., 2013; Byrumet al. 2012b); thus, providing compelling evidence that yFACT islocalized to this chromatin region during transcriptional activation.SptS is an elongation factor that aids RNA polymerase II, while the RSCcomplex of proteins serves as a chromatin remodeler that is involvedwith transcription. Taken together our results present a snapshot of thedynamics of transcriptional activation within a 1 kb viewing window atthe GAL1 promoter chromatin. This analysis demonstrates that theCRISPR-ChAP-MS approach can be used to identify a local epiproteome.

The CRISPR-ChAP-MS approach provides a new tool to study epigeneticregulation. Researchers can now identify proteins and histone PTMs at 1kb resolution using proteomic approaches that do not depend on a prioriknowledge of the protein/PTM target, which distinguishes this methodfrom traditional ChIP. Key to success with chromatin enrichmentprocedures is the quantitative mass spectrometry used to determine whichidentified proteins/PTMs are “specific” to the isolated chromatin. Thesemass spectrometric approaches can be label-free, as used here and in ourTAL-based second generation ChAP methodology (Byrum et al., 2013), orutilize an isotopically heavy label, as used in our LexA-based firstgeneration methodology (Byrum et al. 2012b). Relative to the TAL-basedand LexA-based ChAP methodology, our PrA-Cas9/gRNA approach showedgreatly enhanced enrichment of targeted chromatin, which is instrumentalfor analyzing low copy cellular entities like specific chromatinsections. Furthermore, the Cas9/gRNA system is easily manipulated bysimply altering the gRNA sequence, which provides for adaptability andmultiplexing approaches. Recent and future efforts to further engineerthe specificity of the Cas9/gRNA system will only expand thecapabilities of the CRISPR-ChAP-MS approach (Jiang et al., 2013). Thistechnology is immediately applicable to cell culture and in vivo systemsthat provide for expression of the Cas9/gRNA machinery. TheCRISPR-ChAP-MS approach suggests far-reaching applicability foridentifying molecular components driving chromosomal activities.

Methods for Example 6

Cloning, Western-Blotting, Real-Time Reverse Transcription PCR andChromatin Immunoprecipitation (ChIP).

Cas9 was subcloned from Addgene plasmid 44246 (www.addgene.org/CRISPR/;Cross Lab) into pPrA-LexA (TRP1 selection) (Byrum et al. 2012b)—fusingCas9 with a PrA (Protein A) tag to make pPrA-Cas9. Addgene plasmid 43803(www.addgene.org/CRISPR/; Cross Lab) was used to express the gRNA (URA3selection). The gRNA sequence in the plasmid was mutated in two stepsusing a Stratagene site-directed mutagenesis kit to produce thefollowing sequence matching 20 base-pairs in the GAL1 promoter region:5′ATTTGAAGGTTTGTGGGGCC (SEQ ID NO:372). Three S. cerevisiae strains(W303 matA) were created by transforming the resulting plasmids:pgRNA-GAL1, pPrA-Cas9, and pPrA-Cas9+pgRNA-GAL1. Western-blotting,real-time reverse transcription PCR and chromatin immunoprecipation(ChIP) were as described (Byrum et al. 2013; Byrum et al., 2012b).Off-target sites used in FIG. 10C were: OT1 5′ATGAAAAAATTAGTGGGGCC (SEQID NO:373), OT2 5′ATACGTAGTCTTGTGGGGCC (SEQ ID NO:374), OT35′TACGGAAGGTTGGTGGGGCC (SEQ ID NO:375), OT4 5′TATGTCGCGTTTGTGGGGCC (SEQID NO:376).

CRISPR-ChAP-MS.

S. cerevisiae with pPrA-Cas9 or pPrA-Cas9+gRNA-GAL1 were grown tomid-log phase in synthetic yeast media (minus tryptophan and minustryptophan/uracil respectively) with 3% galactose and subjected to 1.25%formaldehyde cross-linking for 6 minutes. Cross-linking was quenchedwith 125 mM glycine for 5 minutes. Cells were collected bycentrifugation and lysed under cryogenic conditions (Byrum et al.,2012b). Lysate from 10¹⁰ cells was re-suspended in purification buffer(25 mM HEPES-KOH, 0.5 mM EGTA, 1 mM EDTA, 10% glycerol, 0.02% NP-40, 150mM KCl, 1× Sigma fungal protease inhibitor cocktail, 4 μg/mL PepstatinA, 2 mM PMSF) at 5 mL/gram cell lysate. Re-suspended cell lysate wassubjected to sonication with a Bioruptor to shear chromatin to ˜1 kb insize as described (Byrum et al. 2013; Byrum et al. 2012b). PrA-taggedCas9/gRNA complex and associated proteins were affinity purified on 144mg of IgG-coated Dynabeads (Byrum et al. 2013; Byrum et al. 2012b).IgG-coated beads were incubated with lysate for 7 hr at 4° C. withconstant agitation. Beads were collected with magnets and washed twicein purification buffer, once with purification buffer with 1 M NaCl/1 Murea, and once in purification buffer. Proteins were eluted from thewashed beads with 0.5 N ammonium hydroxide/0.5 mM EDTA for 5 minutes atroom temperature. Eluted proteins were lyophilized, re-suspended inLaemmli loading buffer, resolved by 4-20% gradient SDS-PAGE, andvisualized by colloidal Coomassie-staining. Gel lanes were sliced into 2mm sections and subjected to in-gel trypsin digestion (Byrum et al.2012b). Tryptic peptides were analyzed by high resolution tandem massspectrometry with a Thermo Velos Orbitrap mass spectrometer coupled to aWaters nanoACQUITY LC system (Byrum et al. 2013; Byrum et al. 2012b).Proteins and histone PTMs (lysine acetylation and methylation) wereidentified with Mascot (Tables 9 & 10). To determine if a protein was“specific” or “non-specific” to the purification, a previously reportedquantitative mass spectrometry approach was utilized (Byrum et al.2013). In brief, a normalized spectral abundance factor (NSAF) value wascalculated for each protein in the PrA-Cas9 and PrA-Cas9/gRNApurifications. The NSAF value is the number of spectral counts assignedto a given protein (normalized by the molecular weight of that protein)divided by the sum of all normalized spectral counts of all proteinsidentified in the specific purification (Zybailov et al., 2006). Afold-change of normalized NSAF values was then used to identify proteinsspecific to the PrA-Cas9/g RNA purification (Table 9).

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TABLE 1 Proteins identified by Mascot Distiller from ChAP-MS analysis ofGAL1 chromatin isolated from cells grown in glucose. Mascot DistillerQuantitation Report Mascot search results: Glucose Log ratio versus Logratio versus Intensity (all Intensity (selected positive ratios) ratios)L/ 0 1.00e+7 2.00e+7 0 5.00e+6 1.00e+7 (L + 3.00e+7 4.00e+7 −15 1.50e+72.00e+7 −4 −3 H) −10 −5 0 5 −2 −1 0 1 Hit Accession Score Mass L/(L + H)SD (geo) # 1 P00925 1180 46885 0.5797 1.009 7 ENO2_YEAST Enolase 2 OS= Saccharomyces cerevisiae GN = ENO2 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2ANLDVKDQK 0.8222 0.03008 0.05098 0.4849 14020.00 2 3 YDLDFKNPESDK 0.48860.04889 0.1516 0.7 2.59E+05 3 2 YDLDFKNPESDK X 0.5785 0.01343 0.20620.9094 1.62E+05 4 2 AVDDFLLSLDGTANK X 0.5762 0.001 0.2292 0.99421.02E+07 5 3 AVDDFLLSLDGTANK X 0.5799 0.00158 0.6342 0.9975 8.26E+05 6 2DGKYDLDFKNPESDK X 0.5622 0.00842 0.1735 0.989 1.71E+05 7 2GVMNAVNNVNNVIAAAFVK 0.7536 0.05322 0.594 0.4909 2.12E+05 8 3YPIVSIEDPFAEDDWEAWSHF X 0.5768 0 0.8459 0.9995 2.58E+06 FK 9 3RYPIVSIEDPFAEDDWEAWSH X 0.5641 0.0183 0.5271 0.9778 1.27E+05 FFK 10 3YGASAGNVGDEGGVAPNIQTA X 0.5825 0 0.9229 0.9993 1.78E+07 EEALDLIVDAIK HitAccession Score Mass L/(L + H) SD (geo) # 2 P00924 1117 46773 0.57981.008 5 ENO1_YEAST Enolase 1 OS = Saccharomyces cerevisiae GN = ENO1 PE= 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 ANIDVKDQK 0.8222 0.03008 0.05098 0.48491.40E+04 2 2 AVDDFLISLDGTANK X 0.5762 0.001 0.2292 0.9942 1.02E+07 3 3AVDDFLISLDGTANK X 0.5799 0.00158 0.6342 0.9975 8.26E+05 4 3IEEELGDNAVFAGENFHHGDKL X 0.6064 0.00518 0.5017 0.978 3.82E+05 5 3YPIVSIEDPFAEDDWEAWSHF X 0.5768 0 0.8459 0.9995 2.58E+06 FK 6 3RYPIVSIEDPFAEDDWEAWSH X 0.5641 0.0183 0.5271 0.9778 1.27E+05 FFK 7 3YGASAGNVGDEGGVAPNIQTA X 0.5825 0 0.9229 0.9993 1.78E+07 EEALDLIVDAIK HitAccession Score Mass L/(L + H) SD (geo) # 3 P10592 565 69844 0.5495 10HSP72_YEAST Heat shock protein SSA2 OS = Saccharomyces cerevisiae GN= SSA2 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 ITITNDKGR X 0.9873 0.01520.06237 0.9611 4.21E+04 2 2 NFNDPEVQGDMK X 0.554 0.0076 0.3809 0.96038.52E+05 3 2 FKEEDEKESQR X 0.5702 0.0088 0.0696 0.9865 9.27E+04 4 2NFTPEQISSMVLGK X 0.5605 0.00872 0.1288 0.9508 5.66E+05 5 2LIDVDGKPQIQVEFK X 0.5488 0.00255 0.256 0.9909 4.00E+05 6 3LIDVDGKPQIQVEFK X 0.5555 0.00158 0.624 0.9945 2.37E+06 7 3IINEPTAAAIAYGLDKK X 0.5399 0.00584 0.05784 0.938 3.22E+05 8 3LDKSQVDEIVLVGGSTR X 0.528 0.02077 0.3666 0.7616 7.53E+05 9 3NTISEAGDKLEQADKDAVTK X 0.5444 0.00255 0.3405 0.9868 2.60E+06 10 3TQDLLLLDVAPLSLGIETAGGV X 0.5041 0.07248 0.196 0.9741 1.75E+05 MTK HitAccession Score Mass L/(L + H) SD (geo) # 4 P06169 555 61737 0.55811.008 5 PDC1_YEAST Pyruvate decarboxylase isozyme 1 OS = Saccharomycescerevisiae GN = PDC1 PE = 1 SV = 7 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 NATFPGVQMK X 0.54990.00466 0.3978 0.9842 1.13E+06 2 3 VATTGEWDKLTQDK X 0.5476 0.00455 0.2650.9899 1.17E+06 3 3 LLQTPIDMSLKPNDAESEK X 0.5635 0.00264 0.4617 0.99562.39E+05 4 2 MIEIMLPVFDAPQNLVEQAK X 0.5603 0.0038 0.7877 0.9907 7.07E+065 3 LLQTPIDMSLKPNDAESEKEVI X 0.56 0.00158 0.5686 0.9967 2.71E+06DTILALVK Hit Accession Score Mass L/(L + H) SD (geo) # 5 P10591 55170039 0.5549 9 HSP71_YEAST Heat shock protein SSA1 OS = Saccharomycescerevisiae GN = SSA1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ITITNDKGR X 0.98730.0152 0.06237 0.9611 4.21E+04 2 2 NFNDPEVQADMK X 0.595 0.00755 0.16620.9451 4.27E+05 3 2 FKEEDEKESQR X 0.5702 0.0088 0.0696 0.9865 9.27E+04 42 NFTPEQISSMVLGK X 0.5605 0.00872 0.1288 0.9508 5.66E+05 5 2LIDVDGKPQIQVEFK X 0.5488 0.00255 0.256 0.9909 4.00E+05 6 3LIDVDGKPQIQVEFK X 0.5555 0.00158 0.624 0.9945 2.37E+06 7 3IINEPTAAAIAYGLDKK X 0.5399 0.00584 0.05784 0.938 3.22E+05 8 3LDKSQVDEIVLVGGSTR X 0.528 0.02077 0.3666 0.7616 7.53E+05 9 3TQDLLLLDVAPLSLGIETAGGV X 0.5041 0.07248 0.196 0.9741 1.75E+05 MTK HitAccession Score Mass L/(L + H) SD (geo) # 6 P15108 548 80850 0.4277 10HSC82_YEAST ATP-dependent molecular chaperone HSC82 OS = Saccharomycescerevisiae GN = HSC82 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SPFLDALK X 0.594  0.00899 0.5359 0.9605 4.97E+05 2 3 ALKDILGDQVEK X 0.5513   0.022170.189 0.9214 5.90E+04 3 3 VKEEVQELEELNK X 0.5794   0.01043 0.073420.9201 7.47E+04 4 2 LEEVDEEEEEKKPK 0.1049 999 0.1111 0.1643 2.69E+04 5 2LFLKDDQLEYLEEK X 0.5684   0.02513 0.191 0.9399 5.88E+05 6 3LFLKDDQLEYLEEKR X 0.4997   0.04689 0.1356 0.8192 3.36E+05 7 3TLVDITKDFELEETDEEK X 0.4212   0.04847 0.09843 0.7318 2.17E+05 8 2VFITDEAEDLIPEWLSFVK X 0.5569   0.00991 0.227 0.9585 1.35E+06 9 3VFITDEAEDLIPEWLSFVK X 0.5764   0.00772 0.5192 0.9965 3.80E+05 10 3RVFITDEAEDLIPEWLSFVK X 0.5766   0.02142 0.2893 0.9293 1.19E+05 11 3TLVDITKDFELEETDEEKAER X 0.216   0.1336 0.2606 0.801 1.35E+06 HitAccession Score Mass L/(L + H) SD (geo) # 7 P00560 506 44711 0.5584 4PGK_YEAST Phosphoglycerate kinase OS = Saccharomyces cerevisiae GN= PGK1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 VDFNVPLDGKK X 0.3003 0.011340.1059 0.8842 3.08E+05 2 2 VLENTEIGDSIFDK 0.9928 0.00158 0.8106 0.31293.18E+07 3 2 SSAAGNTVIIGGGDTATVAK X 0.577 0.00158 0.6503 0.9976 1.77E+064 3 GVEVVLPVDFIIADAFSADANTK X 0.6021 0.00634 0.4734 0.9828 1.32E+06 5 2GVEVVLPVDFIIADAFSADANTK X 0.5722 0.00525 0.5529 0.9973 1.42E+06 HitAccession Score Mass L/(L + H) SD (geo) # 8 P00359 492 35724 0.55921.017 5 G3P3_YEAST Glyceraldehyde-3-phosphate dehydrogenase 3 OS= Saccharomyces cerevisiae GN = TDH3 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 ELDTAQKX 0.5482 0.00832 0.1767 0.9264 2.25E+04 2 2 VVDLVEHVAK X 0.5557 0.0010.6963 0.9976 2.33E+06 3 2 YAGEVSHDDK 0.7269 0.01789 0.2422 0.69888.10E+04 4 2 TASGNIIPSSTGAAK X 0.5621 0.00158 0.7985 0.9966 9.13E+06 5 3VPTVDVSVVDLTVK X 0.5299 0.00836 0.3828 0.9782 2.33E+05 6 3YAGEVSHDDKHIIVDGK 0.4138 0.03022 0.1569 0.4338 1.27E+06 7 2YAGEVSHDDKHIIVDGK 0.4604 0.01421 0.386 0.4585 4.81E+05 8 2DPANLPWGSSNVDIAIDSTGV X 0.5497 0.00466 0.5417 0.9953 1.10E+06 FK HitAccession Score Mass L/(L + H) SD (geo) # 9 P00950 289 27592 0.57531.028 4 PMG1_YEAST Phosphoglycerate mutase 1 OS = Saccharomycescerevisiae GN = GPM1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 KVYPDVLYTSK X 0.61330.00839 0.05839 0.9039 9.79E+04 2 2 LLPYWQDVIAK X 0.5686 0.001 0.61240.9984 3.23E+06 3 2 SFDVPPPPIDASSPFSQK X 0.579 0.00467 0.7461 0.97475.95E+06 4 3 RSFDVPPPPIDASSPFSQK X 0.5607 0.0055 0.1214 0.9811 2.74E+05Hit Accession Score Mass L/(L + H) SD (geo) # 10 P00942 273 26779 0.89381.241 4 TPIS_YEAST Triosephosphate isomerase OS = Saccharomycescerevisiae GN = TPI1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 KPQVTVGAQNAYLK X 1 00.6505 0.7407 2.01E+06 2 2 ASGAFTGENSVDQIK X 0.8721 0.00784 0.85790.9988 1.90E+06 3 3 SYFHEDDKFIADK X 0.5635 0.00564 0.2565 0.97912.28E+05 4 2 ASGAFTGENSVDQIKDVGAK X 0.5037 0.05902 0.5738 0.86961.28E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 11 P23254 25874104 0.5924 1.089 4 TKT1_YEAST Transketolase 1 OS = Saccharomycescerevisiae GN = TKL1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 LFSEYQK 0.7783 0.023980.136 0.6468 1.69E+05 2 2 ILAVDTVSK X 0.6661 0.02039 0.1191 0.85146.18E+05 3 3 KFPELGAELAR X 0.4889 0.01828 0.08146 0.9458 3.41E+04 4 2LSGQLPANWESK 0.9991 0.00158 0.5921 0.6509 1.69E+06 5 2 VVSLPDFFTFDK X0.5277 0.01746 0.3974 0.82 4.93E+05 6 2 QNLPQLEGSSIESASK X 0.53950.00842 0.1282 0.9767 9.63E+04 7 2 SFVVPQEVYDHYQK 0.4152 0.04681 0.39120.41 1.50E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 12 P34760251 21688 0.5583 1 TSA1_YEAST Peroxiredoxin TSA1 OS = Saccharomycescerevisiae GN = TSA1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 TAVVDGVFDEVSLDK X0.5583 0.01341 0.4102 0.9415 7.29E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 13 P02994 242 50001 0.5996 5 EF1A_YEAST Elongation factor1-alpha OS = Saccharomyces cerevisiae GN = TEF1 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 FQEIVK X 0.9909 0.00329 0.1232 0.9948 5.97E+05 2 2 LPLQDVYK X 0.52660.002 0.5985 0.9845 4.55E+06 3 3 SHINVVVIGHVDSGK X 0.5427 0.010930.07069 0.9813 4.33E+04 4 3 TLLEAIDAIEQPSRPTDKPLR X 0.6222 0.01 0.38090.7963 1.58E+07 5 3 SVEMHHEQLEQGVPGDNVGF X 0.5271 0.00255 0.8205 0.99722.24E+06 NVK Hit Accession Score Mass L/(L + H) SD (geo) # 14 P11484 23566937 0.5697 1.042 3 HSP75_YEAST Heat shock protein SSB1 OS= Saccharomyces cerevisiae GN = SSB1 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2LLSDFFDGK X 0.5313 0.004 0.3939 0.9936 1.18E+06 2 2 VIDVDGNPVIEVQYLEETKX 0.5573 0.03139 0.2885 0.9312 2.81E+05 3 3 STSGNTHLGGQDFDTNLLEHFK X0.6018 0.01912 0.5754 0.975 1.64E+06 Hit Accession Score Mass L/(L + H)SD (geo) # 15 P16521 220 115920 0.4751 1.086 3 EF3A_YEAST Elongationfactor 3A OS = Saccharomyces cerevisiae GN = YEF3 PE = 1 SV = 3 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 QINENDAEAMNK X 0.502 0.03789 0.1931 0.9204 1.87E+05 22 ATETVDNKDIER X 0.5572 0.01016 0.3336 0.9535 2.92E+05 3 2LVEDPQVIAPFLGK X 0.4314 0.01731 0.1193 0.9722 5.89E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 16 P14540 217 39812 0.5455 1.017 4ALF_YEAST Fructose-bisphosphate aldolase OS = Saccharomyces cerevisiaeGN = FBA1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LLPWFDGMLEADEAYFK X 0.53870.01791 0.6343 0.9901 2.73E+06 2 3 LLPWFDGMLEADEAYFK X 0.5693 0.003240.7442 0.9942 4.58E+05 3 2 KLLPWFDGMLEADEAYFK X 0.5497 0.02627 0.30490.8469 4.81E+04 4 3 KLLPWFDGMLEADEAYFK X 0.5579 0.00588 0.6699 0.99196.41E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 17 P05750 21426630 0.5144 1 RS3_YEAST 40S ribosomal protein S3 OS = Saccharomycescerevisiae GN = RPS3 PE = 1 SV = 5 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 ALPDAVTIIEPKEEEPILAPSVKX 0.5144 0.00787 0.0782 0.9853 1.22E+06 Hit Accession Score Mass L/(L+ H) SD (geo) # 18 P38788 196 58515 0.5268 1.003 2 SSZ1_YEASTRibosome-associated complex subunit SSZ1 OS = Saccharomyces cerevisiaeGN = SSZ1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 EAVLTVPTNFSEEQK X 0.5251 0.005740.2728 0.9966 3.66E+05 2 3 LISDYDADELAEALQPVIVNTP X 0.5276 0.005570.6012 0.9986 7.77E+05 HLK Hit Accession Score Mass L/(L + H) SD (geo) #19 P40150 195 66930 0.5697 1.042 3 HSP76_YEAST Heat shock protein SSB2OS = Saccharomyces cerevisiae GN = SSB2 PE = 1 SV = 2 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2LLSDFFDGK X 0.5313 0.004 0.3939 0.9936 1.18E+06 2 2 VIDVDGNPVIEVQYLEETKX 0.5573 0.03139 0.2885 0.9312 2.81E+05 3 3 STSGNTHLGGQDFDTNLLEHFK X0.6018 0.01912 0.5754 0.975 1.64E+06 Hit Accession Score Mass L/(L + H)SD (geo) # 20 P32324 189 93719 0.4948 1.141 4 EF2_YEAST Elongationfactor 2 OS = Saccharomyces cerevisiae GN = EFT1 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 TGTLTTSETAHNMK X 0.5494 0.05488 0.2574 0.9685 3.09E+042 2 ETVESESSQTALSK X 0.4964 0.00945 0.5999 0.989 1.00E+06 3 3WTNKDTDAEGKPLER X 0.4881 0.01896 0.04008 0.9109 1.19E+05 4 2WTNKDTDAEGKPLER X 0.383 0.06499 0.03736 0.93 1.87E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 21 P32589 184 77318 0 HSP7F_YEAST Heatshock protein homolog SSE1 OS = Saccharomyces cerevisiae GN = SSE1 PE= 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 QVEDEDHMEVFPAGSSFPSTK 0.6809 0.02791 0.30310.3098 9.21E+05 2 3 QSISEAFGKPLSTTLNQDEAIAK 0.5365 0.06281 0.4112 0.27453.29E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 22 P54115 18354380 0.6157 1 ALDH6_YEAST Magnesium-activated aldehyde dehydrogenase,cytosolic OS = Saccharomyces cerevisiae GN = ALD6 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 SAHLVFDDANIKK X 0.6157 0.0168 0.06354 0.9683 1.83E+042 3 IVKEEIFGPVVTVAK −0.01367 0.6603 0.692 0.03687 2.37E+06 Hit AccessionScore Mass L/(L + H) SD (geo) # 23 P00360 179 35728 0.5624 1.059 4G3P1_YEAST Glyceraldehyde-3-phosphate dehydrogenase 1 OS = Saccharomycescerevisiae GN = TDH1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ELDTAQK X 0.54820.00832 0.1767 0.9264 2.25E+04 2 2 TASGNIIPSSTGAAK X 0.5621 0.001580.7985 0.9966 9.13E+06 3 3 VPTVDVSVVDLTVK X 0.5299 0.00836 0.3828 0.97822.33E+05 4 3 IATYQERDPANLPWGSLK X 0.6109 0.00894 0.4762 0.9875 2.36E+05Hit Accession Score Mass L/(L + H) SD (geo) # 24 P05694 159 86296 0.54741.143 4 METE_YEAST 5-methyltetrahydropteroyltriglutamate--homocysteinemethyltransferase OS = Saccharomyces cerevisiae GN = MET6 PE = 1 SV = 4z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 VATSGVANK X 0.4292 0.05981 0.2367 0.7626 5.78E+05 2 2ITVDELFK X 0.7613 0.02167 0.4122 0.9349 3.00E+05 3 2 ALDADVVSIEFSK X0.5995 0.00506 0.3617 0.9908 4.15E+05 4 3 APEQFDEVVAAIGNK X 0.57690.02178 0.2145 0.9228 7.39E+04 Hit Accession Score Mass L/(L + H) SD(geo) # 25 P00817 159 32280 0.3148 1.707 2 IPYR_YEAST Inorganicpyrophosphatase OS = Saccharomyces cerevisiae GN = IPP1 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 LNDIEDVEK X 0.1915 0.08967 0.192 0.967 2.15E+05 2 3LEITKEETLNPIIQDTKK 0.5691 0.01513 0.1321 0.6614 3.55E+04 3 3AVGDNDPIDVLEIGETIAYTGQ X 0.5565 0.00915 0.5386 0.9951 1.89E+05 VK HitAccession Score Mass L/(L + H) SD (geo) # 26 P46655 156 81369 0.42151.269 2 SYEC_YEAST Glutamyl-tRNA synthetase, cytoplasmic OS= Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2KNDDGSMVAK X 0.5902 0.05607 0.0228 0.8152 515.7 2 3 EKEEFQDSILEDLDLLGIKX 0.4214 0.04183 0.2818 0.7588 6.23E+05 Hit Accession Score Mass L/(L+ H) SD (geo) # 27 P09436 156 123651 0.9973 1 SYIC_YEAST Isoleucyl-tRNAsynthetase, cytoplasmic OS = Saccharomyces cerevisiae GN = ILS1 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 MSNIDFQYDDSVK X 0.9973 0.00158 0.6248 0.9613.01E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 28 P61864 1488552 0.8538 1 UBIQ_YEAST Ubiquitin OS = Saccharomyces cerevisiae GN= UBI1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 IQDKEGIPPDQQR X 0.8538 0.012760.1534 0.8756 1.67E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 29P04456 146 15748 0.5126 1 RL25_YEAST 60S ribosomal protein L25 OS= Saccharomyces cerevisiae GN = RPL25 PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2ELYEVDVLK X 0.5126 0.00785 0.1734 0.9804 4.97E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 30 P12709 146 61261 0.5947 3 G6PI_YEASTGlucose-6-phosphate isomerase OS = Saccharomyces cerevisiae GN = PGI1 PE= 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 NWFLSK X 0.5893 0.01445 0.08506 0.89651.22E+04 2 2 TFTTAETITNANTAK 0.7863 0.02669 0.2797 0.4859 1.42E+05 3 2NLVNDEIIAALIELAK X 0.7445 0.01763 0.05341 0.9308 1.58E+04 4 3ANKPMYVDGVNVAPEVDSVLK X 0.5898 0.03119 0.315 0.7014 4.18E+05 HitAccession Score Mass L/(L + H) SD (geo) # 31 P08524 145 40738 0.5181 1FPPS_YEAST Farnesyl pyrophosphate synthase OS = Saccharomyces cerevisiaeGN = FPP1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 TVEQLGQEEYEK X 0.5181 0.005850.1843 0.9906 4.80E+05 2 2 IEQLYHEYEESIAK 0.3587 0.08308 0.1586 0.62976.38E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 32 P00330 14236800 0.5295 1.039 3 ADH1_YEAST Alcohol dehydrogenase 1 OS= Saccharomyces cerevisiae GN = ADH1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2ANELLINVK X 0.5781 0.01445 0.406 0.9865 4.01E+05 2 2 VVGLSTLPEIYEK X0.518 0.001 0.6074 0.9963 5.17E+06 3 3 VLGIDGGEGKEELFR X 0.5414 0.004030.7131 0.9802 3.52E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 33P07262 138 49763 0.2171 1 DHE4_YEAST NADP-specific glutamatedehydrogenase 1 OS = Saccharomyces cerevisiae GN = GDH1 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 VTWENDKGEQEVAQGYR X 0.2171 0.1184 0.5086 0.76666.81E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 34 P31373 13842692 0.6023 1.05 2 CYS3_YEAST Cystathionine gamma-lyase OS= Saccharomyces cerevisiae GN = CYS3 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2ISVGIEDTDDLLEDIK X 0.613 0.00887 0.1862 0.967 6.82E+05 2 3ISVGIEDTDDLLEDIKQALK X 0.5634 0.01345 0.3481 0.9112 1.80E+05 HitAccession Score Mass L/(L + H) SD (geo) # 35 P22202 137 70009 0.58321.457 2 HSP74_YEAST Heat shock protein SSA4 OS = Saccharomycescerevisiae GN = SSA4 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ITITNDKGR X 0.98730.0152 0.06237 0.9611 4.21E+04 2 3 IINEPTAAAIAYGLDKK X 0.5399 0.005840.05784 0.938 3.22E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 36A6ZP47 134 65697 0.3172 1 DED1_YEAS7 ATP-dependent RNA helicase DED1 OS= Saccharomyces cerevisiae (strain YJM789) GN = DED1 PE = 3 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 TGGFLFPVLSESFK X 0.3172 0.03297 0.08265 0.80193.08E+05 2 3 DVPEPITEFTSPPLDGLLLENIK 0.00052 7.122 0.6671 0.16591.16E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 37 P00549 13454510 0.5402 2.375 2 KPYK1_YEAST Pyruvate kinase 1 OS = Saccharomycescerevisiae GN = PYK1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 EVLGEQGKDVK 0.82110.01418 0.5587 0.4163 9.19E+05 2 3 MNFSHGSYEYHK X 0.159 0.3656 0.2330.8491 3.57E+04 3 3 GVNLPGTDVDLPALSEKDKED X 0.5499 0.00705 0.3217 0.96342.45E+06 LR Hit Accession Score Mass L/(L + H) SD (geo) # 38 P29311 13430073 0.5686 1.063 3 BMH1_YEAST Protein BMH1 OS = Saccharomycescerevisiae GN = BMH1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 LAEQAERYEEMVENMK X0.6493 0.01923 0.1302 0.8619 2.33E+04 2 3 QAFDDAIAELDTLSEESYK X 0.57980.00382 0.3875 0.9933 2.42E+05 3 3 ISDDILSVLDSHLIPSATTGESK X 0.56430.01199 0.1289 0.8075 1.04E+06 Hit Accession Score Mass L/(L + H) SD(geo) # 39 P26321 133 33890 0 RL5_YEAST 60S ribosomal protein L5 OS= Saccharomyces cerevisiae GN = RPL5 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 40 P26263 130 61542 0PDC6_YEAST Pyruvate decarboxylase isozyme 3 OS = Saccharomycescerevisiae GN = PDC6 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 41 A6ZQJ1 121 44837 0.5295 1 IF4A_YEAS7ATP-dependent RNA helicase eIF4A OS = Saccharomyces cerevisiae (strainYJM789) GN = TIF1 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 AIMPIIEGHDVLAQAQSGTGK X0.5295 0.00498 0.5721 0.9845 4.30E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 42 Q02753 119 18231 0.4842 1 RL21A_YEAST 60S ribosomalprotein L21-A OS = Saccharomyces cerevisiae GN = RPL21A PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 VGDIVDIK X 0.4842 0.00614 0.01566 0.9582 1.27E+05 HitAccession Score Mass L/(L + H) SD (geo) # 43 P05030 119 99941 0.5928 1PMA1_YEAST Plasma membrane ATPase 1 OS = Saccharomyces cerevisiae GN= PMA1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 TVEEDHPIPEDVHENYENK X 0.59280.02245 0.3764 0.8651 3.27E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 44 Q03195 119 68297 0 RLI1_YEAST Translation initiation factorRLI1 OS = Saccharomyces cerevisiae GN = RLI1 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 LLAGALKPDEGQDIPK 0.1154 0.2281 0.1563 0.679 1.09E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 45 P38011 119 34936 0.4788 1 GBLP_YEASTGuanine nucleotide-binding protein subunit beta-like protein OS= Saccharomyces cerevisiae GN = ASC1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3VVPNEKADDDSVTIISAGNDK X 0.4788 0.00934 0.03497 0.9434 2.43E+05 HitAccession Score Mass L/(L + H) SD (geo) # 46 P19097 117 206818 0.6972 1FAS2_YEAST Fatty acid synthase subunit alpha OS = Saccharomycescerevisiae GN = FAS2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 EIYYTPDPSELAAK X 0.69720.02896 0.2436 0.8764 4.39E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 47 P22768 116 47175 0 ASSY_YEAST Argininosuccinate synthase OS= Saccharomyces cerevisiae GN = ARG1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 48 P41277 112 28138 0.51931.003 2 GPP1_YEAST (DL)-glycerol-3-phosphatase 1 OS = Saccharomycescerevisiae GN = GPP1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 FAPDFADEEYVNK 0.26220.08634 0.2384 0.6536 3.56E+05 2 3 FAPDFADEEYVNKLEGEIPEK X 0.51890.00547 0.2526 0.9631 1.44E+06 3 2 VGEYNAETDEVELIFDDYLYAK X 0.52170.01439 0.5462 0.9935 2.38E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 49 P49090 110 64857 0.5527 1.053 2 ASNS2_YEAST Asparaginesynthetase [glutamine-hydrolyzing] 2 OS = Saccharomyces cerevisiae GN= ASN2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 YFTPDWLDEK X 0.5819 0.020380.1065 0.9343 3.09E+05 2 3 AFDTTDEPDVKPYLPEEILWR X 0.5251 0.03417 0.25620.9393 3.11E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 50 P15624110 67691 0.9837 1.076 3 SYFB_YEAST Phenylalanyl-tRNA synthetase betachain OS = Saccharomyces cerevisiae GN = FRS1 PE = 1 SV = 3 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 SKEGAEPK X 0.9916 0.00141 0.07152 0.9856 1.79E+06 2 2 GYWIEEDDSVK X0.8641 0.05554 0.05094 0.8192 3.24E+04 3 2 NSGFEIIQGLLGK X 0.87040.03036 0.142 0.8105 8.54E+04 Hit Accession Score Mass L/(L + H) SD(geo) # 51 P19882 109 60714 0.4595 1 HSP60_YEAST Heat shock protein 60,mitochondrial OS = Saccharomyces cerevisiae GN = HSP60 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 NVLIEQPFGPPK 0.3833 0.07553 0.1289 0.6499 8.66E+04 2 2AAVEEGILPGGGTALVK X 0.4595 0.03115 0.1117 0.9559 1.38E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 52 P38088 109 75845 0 SYG_YEASTGlycyl-tRNA synthetase 1 OS = Saccharomyces cerevisiae GN = GRS1 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) # 53P07284 105 53276 0 SYSC_YEAST Seryl-tRNA synthetase, cytoplasmic OS= Saccharomyces cerevisiae GN = SES1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 54 P53184 99 24978 0.4323 1PNC1_YEAST Nicotinamidase OS = Saccharomyces cerevisiae GN = PNC1 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 TTVLLDYTRPISDDPEVINK X 0.4323 0.02539 0.28140.7218 1.46E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 55 P3600899 46827 0.8918 1.457 2 EF1G2_YEAST Elongation factor 1-gamma 2 OS= Saccharomyces cerevisiae GN = TEF4 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2LLGSDVIEK X 0.9663 0.00996 0.4982 0.9961 1.44E+06 2 2 WFNTVAASPIVK X0.527 0.01203 0.07669 0.8876 2.21E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 56 Q01560 95 45444 0 NOP3_YEAST Nucleolar protein 3 OS= Saccharomyces cerevisiae GN = NPL3 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 57 P40213 94 15974 0RS16_YEAST 40S ribosomal protein S16 OS = Saccharomyces cerevisiae GN= RPS16A PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 YVDEQSKNELK 0.9917 0.004340.3579 0.08027 4.77E+05 2 2 YVDEQSKNELKK 0.9999 0.00574 0.1204 0.11644.58E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 58 P16140 9457922 0 VATB_YEAST V-type proton ATPase subunit B OS = Saccharomycescerevisiae GN = VMA2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 59 P25293 93 47855 0.5024 1 NAP1_YEAST Nucleosomeassembly protein OS = Saccharomyces cerevisiae GN = NAP1 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 LGSLVGQDSGYVGGLPK X 0.5024 0.03188 0.08129 0.7582.53E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 60 P41940 9339781 0.5624 1.009 2 MPG1_YEAST Mannose-1-phosphate guanyltransferase OS= Saccharomyces cerevisiae GN = MPG1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2LATGANIVGNALIDPTAK X 0.5695 0.00687 0.05507 0.9887 2.54E+04 2 3INAGLYILNPEVIDLIEMKPTSIEK X 0.562 0.00414 0.5133 0.9966 4.50E+05 HitAccession Score Mass L/(L + H) SD (geo) # 61 P15705 93 66705 0STI1_YEAST Heat shock protein STI1 OS = Saccharomyces cerevisiae GN= STI1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 62 Q03048 91 15979 0 COFI_YEAST Cofilin OS = Saccharomycescerevisiae GN = COF1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SGVAVADESLTAFNDLK0.2984 0.1196 0.0948 0.4874 1.00E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 63 P38707 90 62168 0.6442 1 SYNC_YEAST Asparaginyl-tRNAsynthetase, cytoplasmic OS = Saccharomyces cerevisiae GN = DED81 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 SVQYVLEDPIAGPLVK X 0.6442 0.02511 0.1820.8768 2.97E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 64 P4908989 64734 0.4454 1.252 2 ASNS1_YEAST Asparagine synthetase[glutamine-hydrolyzing] 1 OS = Saccharomyces cerevisiae GN = ASN1 PE = 1SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 YFTPDWLDEK X 0.5819 0.02038 0.1065 0.93433.09E+05 2 2 ATNDVEPSTYDSK X 0.375 0.01032 0.3126 0.9726 4.80E+05 HitAccession Score Mass L/(L + H) SD (geo) # 65 P14832 88 17380 0CYPH_YEAST Peptidyl-prolyl cis-trans isomerase OS = Saccharomycescerevisiae GN = CPR1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 KVESLGSPSGATK 0.55980.00415 0.2553 0.5249 4.83E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 66 P0C0W9 86 19844 0.3135 1 RL11A_YEAST 60S ribosomal proteinL11-A OS = Saccharomyces cerevisiae GN = RPL11A PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 VLEQLSGQTPVQSK 0.000776 0.4364 0.8707 0.2733 1.50E+07 2 3VLEQLSGQTPVQSK X 0.3135 0.169 0.1611 0.8233 1.39E+04 Hit Accession ScoreMass L/(L + H) SD (geo) # 67 P14120 84 11504 0.5841 1 RL30_YEAST 60Sribosomal protein L30 OS = Saccharomyces cerevisiae GN = RPL30 PE = 1 SV= 3 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 VYYFQGGNNELGTAVGK X 0.5841 0.02582 0.205 0.89889.20E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 68 P26755 8413863 0 RFA3_YEAST Replication factor A protein 3 OS = Saccharomycescerevisiae GN = RFA3 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 69 P04147 83 64304 0 PABP_YEASTPolyadenylate-binding protein, cytoplasmic and nuclear OS= Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2TAEQLENLNIQDDQK 0.001099 1.859 0.4682 0.9671 3.84E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 70 P32527 82 49439 0 ZUO1_YEAST ZuotinOS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 71 P38625 82 58750 0.5454 1GUAA_YEAST GMP synthase [glutamine-hydrolyzing] OS = Saccharomycescerevisiae GN = GUA1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 VTYDITSKPPATVEWE X0.5454 0.01078 0.239 0.9456 3.32E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 72 P31412 80 44434 0.6452 1 VATC_YEAST V-type proton ATPasesubunit C OS = Saccharomyces cerevisiae GN = VMA5 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 IGSLDTLIVESEELSK X 0.6452 0.01519 0.07177 0.97532.77E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 73 P05753 8029608 0 RS4_YEAST 40S ribosomal protein S4 OS = Saccharomyces cerevisiaeGN = RPS4A PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 74 P26783 79 25023 0.4952 1 RS5_YEAST 40S ribosomal proteinS5 OS = Saccharomyces cerevisiae GN = RPS5 PE = 1 SV = 3 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 TIAETLAEELINAAK X 0.4952 0.0071 0.5691 0.9574 1.53E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 75 P17076 76 28396 0 RL8A_YEAST 60Sribosomal protein L8-A OS = Saccharomyces cerevisiae GN = RPL8A PE = 1SV = 4 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) # 76P53030 76 24470 0.5139 1 RL1_YEAST 60S ribosomal protein L1 OS= Saccharomyces cerevisiae GN = RPL1A PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2FPTPVSHNDDLYGK X 0.5139 0.02598 0.07442 0.8939 3.55E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 77 P25694 74 92331 0.5765 1 CDC48_YEASTCell division control protein 48 OS = Saccharomyces cerevisiae GN= CDC48 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 AAAPTVVFLDELDSIAK X 0.57650.01988 0.2107 0.9888 1.27E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 78 P40303 73 28574 0 PSA7_YEAST Proteasome component PRE6 OS= Saccharomyces cerevisiae GN = PRE6 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 79 P16861 73 108408 0K6PF1_YEAST 6-phosphofructokinase subunit alpha OS = Saccharomycescerevisiae GN = PFK1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 80 P35691 73 18729 0 TCTP_YEASTTranslationally-controlled tumor protein homolog OS = Saccharomycescerevisiae GN = TMA19 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 LQETNPEEVPKFEK 0.015740.05686 0.3046 0.3037 2.21E+06 Hit Accession Score Mass L/(L + H) SD(geo) # 81 P05738 72 21556 0.6443 1 RL9A_YEAST 60S ribosomal proteinL9-A OS = Saccharomyces cerevisiae GN = RPL9A PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 FLDGIYVSHK X 0.6443 0.01495 0.1913 0.8882 2.99E+04 2 3YIQTEQQIEVPEGVTVSIK 0.008727 0.6329 0.355 0.4397 1.88E+06 Hit AccessionScore Mass L/(L + H) SD (geo) # 82 P00899 71 56732 0 TRPE_YEASTAnthranilate synthase component 1 OS = Saccharomyces cerevisiae GN= TRP2 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 83 P17079 71 17956 0.5847 1 RL12_YEAST 60S ribosomal proteinL12 OS = Saccharomyces cerevisiae GN = RPL12A PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 VDFKNPHDIIEGINAGEIEIPEN X 0.5847 0.02535 0.1429 0.8697 3.12E+05 HitAccession Score Mass L/(L + H) SD (geo) # 84 P07806 70 126596 0.40011.235 2 SYV_YEAST Valyl-tRNA synthetase, mitochondrial OS= Saccharomyces cerevisiae GN = VAS1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2TGVFEPEFTADGK X 0.365 0.03845 0.2789 0.8561 4.52E+05 2 2 LNTAISNLEVENK X0.5312 0.02003 0.0767 0.9905 1.46E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 85 P26781 70 17898 0.4992 1 RS11_YEAST 40S ribosomal proteinS11 OS = Saccharomyces cerevisiae GN = RPS11A PE = 1 SV = 3 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 TAIEGSYIDKK X 0.4992 0.0041 0.1365 0.9905 1.73E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 86 P53252 70 38326 0.5822 1 PIL1_YEASTSphingolipid long chain base-responsive protein PIL1 OS = Saccharomycescerevisiae GN = PIL1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 APTASQLQNPPPPPSTTK X0.5822 0.02737 0.2412 0.8526 1.83E+04 Hit Accession Score Mass L/(L + H)SD (geo) # 87 P22943 68 11686 0 HSP12_YEAST 12 kDa heat shock protein OS= Saccharomyces cerevisiae GN = HSP12 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2GKDNAEGQGESLADQAR 0.01324 0.7291 0.2434 0.4791 3.47E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 88 P02407 67 15891 0 RS17A_YEAST 40Sribosomal protein S17-A OS = Saccharomyces cerevisiae GN = RPS17A PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) # 89P04801 66 84467 0 SYTC_YEAST Threonyl-tRNA synthetase, cytoplasmic OS= Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2TVSQADFPGLEGVAK 0.9625 0.01322 0.639 0.3281 3.05E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 90 P09733 63 49945 0 TBA1_YEAST Tubulinalpha-1 chain OS = Saccharomyces cerevisiae GN = TUB1 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 91 P33204 6219959 0 ARPC4_YEAST Actin-related protein 2/3 complex subunit 4 OS= Saccharomyces cerevisiae GN = ARC19 PE = 1 SV = 2 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 92 P23301 62 17208 0.4447 1IF5A2_YEAST Eukaryotic translation initiation factor 5A-2 OS= Saccharomyces cerevisiae GN = HYP2 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3KLEDLSPSTHNMEVPVVK X 0.4447 0.02507 0.3275 0.7978 8.63E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 93 P06168 61 44565 0 ILV5_YEASTKetol-acid reductoisomerase, mitochondrial OS = Saccharomyces cerevisiaeGN = ILV5 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 94 P05744 59 12219 0.6527 1 RL33A_YEAST 60S ribosomal proteinL33-A OS = Saccharomyces cerevisiae GN = RPL33A PE = 1 SV = 3 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 IEGVATPQDAQFYLGK X 0.6527 0.01745 0.2096 0.9659 1.36E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 95 P04807 58 53908 0.6227 1 HXKB_YEASTHexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 TKYDITIDEESPRPGQQTFEK X 0.6227 0.02524 0.2555 0.89187.65E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 96 P03965 58124439 0 CARB_YEAST Carbamoyl-phosphate synthase arginine-specific largechain OS = Saccharomyces cerevisiae GN = CPA2 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity ModificationsHit Accession Score Mass L/(L + H) SD (geo) # 97 Q00955 58 250197 0ACAC_YEAST Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae GN= FAS3 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 IGSFGPQEDEFFNK 0.8663 0.021990.1144 0.6383 4.24E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 98P32598 58 35884 0.499 1 PP12_YEAST Serine/threonine-protein phosphatasePP1-2 OS = Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 GSKPGQQVDLEENEIR X 0.499 0.03409 0.1183 0.9862 2959 Hit AccessionScore Mass L/(L + H) SD (geo) # 99 P02365 58 27204 0.4787 1 RS6_YEAST40S ribosomal protein S6 OS = Saccharomyces cerevisiae GN = RPS6A PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 KGEQELEGLTDTTVPK X 0.4787 0.01467 0.03970.9854 2.01E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 100 P3701257 63049 0 PGM2_YEAST Phosphoglucomutase-2 OS = Saccharomyces cerevisiaeGN = PGM2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 IIKDFPELDLGTIGK 0.6291 0.027280.1059 0.6921 5.18E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 101P10664 57 39325 0.482 1.07 2 RL4A_YEAST 60S ribosomal protein L4-A OS= Saccharomyces cerevisiae GN = RPL4A PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2IPEIPLVVSTDLESIQK X 0.4871 0.01446 0.3459 0.9946 8.51E+05 2 3IINSSEIQSAIRPAGQATQK X 0.4381 0.02184 0.2528 0.953 9.33E+04 HitAccession Score Mass L/(L + H) SD (geo) # 102 P17536 55 23527 0TPM1_YEAST Tropomyosin-1 OS = Saccharomyces cerevisiae GN = TPM1 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 QTEQDNVEKENQIK 0.4204 0.1271 0.03615 0.49531.04E+04 2 3 NKDLEQENVEKENQIK 0.438 0.04989 0.1615 0.6221 6.92E+04 HitAccession Score Mass L/(L + H) SD (geo) # 103 P32469 55 33970 0DPH5_YEAST Diphthine synthase OS = Saccharomyces cerevisiae GN = DPH5 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) #104 P35271 54 17115 0.5135 1 RS18_YEAST 40S ribosomal protein S18 OS= Saccharomyces cerevisiae GN = RPS18A PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3QNDITDGKDYHTLANNVESK X 0.5135 0.01629 0.07641 0.9441 5.50E+04 HitAccession Score Mass L/(L + H) SD (geo) # 105 P13663 54 39735 0DHAS_YEAST Aspartate-semialdehyde dehydrogenase OS = Saccharomycescerevisiae GN = HOM2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 106 P54839 53 54979 0 HMCS_YEASTHydroxymethylglutaryl-CoA synthase OS = Saccharomyces cerevisiae GN= ERG13 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 DYDESLTDKNIEK 0.1337 0.17370.3775 0.4027 2.38E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 107P40016 53 60385 0 RPN3_YEAST 26S proteasome regulatory subunit RPN3 OS= Saccharomyces cerevisiae GN = RPN3 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 108 P05317 52 33866 0.5164 1RLA0_YEAST 60S acidic ribosomal protein P0 OS = Saccharomyces cerevisiaeGN = RPP0 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 GTIEIVSDVK X 0.5164 0.007780.1538 0.9872 4.30E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 109P15992 51 23865 0 HSP26_YEAST Heat shock protein 26 OS = Saccharomycescerevisiae GN = HSP26 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 NQILVSGEIPSTLNEESKDK0.6438 0.03278 0.3187 0.6599 2.01E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 110 P32481 50 57829 0 IF2G_YEAST Eukaryotic translationinitiation factor 2 subunit gamma OS = Saccharomyces cerevisiae GN= GCD11 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 LGDEIEIRPGIVTK 0.6051 0.097360.2626 0.3614 1.13E+05 2 3 VAFTGLEEDGETEEEKR 0.3223 0.05784 0.093510.5764 1.71E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 111 P4105649 12233 0 RL33B_YEAST 60S ribosomal protein L33-B OS = Saccharomycescerevisiae GN = RPL33B PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2 IEGVATPQEAQFYLGK0.000032 376.9 0.3763 0.1226 1.13E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 112 P14126 49 44075 0 RL3_YEAST 60S ribosomal protein L3 OS= Saccharomyces cerevisiae GN = RPL3 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 113 B3LLJ2 49 29059 0.5829 1RS3A2_YEAS1 40S ribosomal protein S1-B OS = Saccharomyces cerevisiae(strain RM11-1a) GN = RPS1B PE = 3 SV = 1 z Sequence Incl. L/(L + H)Std. Err. Fraction Correlation Intensity Modifications 1 2 VSGFKDEVLETVX 0.5829 0.0184 0.1617 0.9565 4.47E+05 Hit Accession Score Mass L/(L+ H) SD (geo) # 114 P35997 49 8930 0 RS27A_YEAST 40S ribosomal proteinS27-A OS = Saccharomyces cerevisiae GN = RPS27A PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity ModificationsHit Accession Score Mass L/(L + H) SD (geo) # 115 P39954 48 49094 0.17861 SAHH_YEAST Adenosylhomocysteinase OS = Saccharomyces cerevisiae GN= SAH1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 LKVPAINVNDSVTK X 0.1786 0.12650.1537 0.7426 1.16E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 116P05736 48 27392 0.5256 1 RL2_YEAST 60S ribosomal protein L2 OS= Saccharomyces cerevisiae GN = RPL2A PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3ASLNVGNVLPLGSVPEGTIVS X 0.5256 0.00852 0.3563 0.9201 1.23E+06 NVEEKPGDRHit Accession Score Mass L/(L + H) SD (geo) # 117 Q12306 47 11662 0SMT3_YEAST Ubiquitin-like protein SMT3 OS = Saccharomyces cerevisiae GN= SMT3 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 118 O14467 47 16394 0.7594 1 MBF1_YEAST Multiprotein-bridgingfactor 1 OS = Saccharomyces cerevisiae GN = MBF1 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 INEKPTVVNDYEAAR X 0.7594 0.04153 0.08694 0.78151.61E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 119 Q08438 4673997 0 VHS3_YEAST Protein VHS3 OS = Saccharomyces cerevisiae GN = VHS3PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) #120 P38708 46 77337 0.3265 1 YHI0_YEAST Putative prolyl-tRNA synthetaseYHR020W OS = Saccharomyces cerevisiae GN = YHR020W PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 IPEILEEMQGDLFK X 0.3265 0.09196 0.1283 0.9662 6.43E+04Hit Accession Score Mass L/(L + H) SD (geo) # 121 P40069 44 1229810.8151 1 IMB4_YEAST Importin subunit beta-4 OS = Saccharomycescerevisiae GN = KAP123 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 3 FHEEYLPLIIDIIDSAKX 0.8151 0.02809 0.2967 0.9444 3.29E+04 Hit Accession Score Mass L/(L+ H) SD (geo) # 122 P05737 42 27621 0.5221 1 RL7A_YEAST 60S ribosomalprotein L7-A OS = Saccharomyces cerevisiae GN = RPL7A PE = 1 SV = 3 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 ATLELLK X 0.5221 0.00509 0.1793 0.9871 8.87E+04 HitAccession Score Mass L/(L + H) SD (geo) # 123 P38715 42 37095 0.03996 1GRE3_YEAST NADPH-dependent aldose reductase GRE3 OS = Saccharomycescerevisiae GN = GRE3 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 TTPTLFENDVIK X 0.039960.4915 0.0985 0.8748 1.48E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 124 P15019 40 37302 0.5972 1 TAL1_YEAST Transaldolase OS= Saccharomyces cerevisiae GN = TAL1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3DYKGEADPGVISVK X 0.5972 0.01513 0.05713 0.9284 1.93E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 125 P39939 40 13438 0 RS26B_YEAST 40Sribosomal protein S26-B OS = Saccharomyces cerevisiae GN = RPS26B PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 DLSEASVYPEYALPK 0.4244 0.02522 0.097770.5891 8.08E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 126 P2544340 27433 0.4963 1 RS2_YEAST 40S ribosomal protein S2 OS = Saccharomycescerevisiae GN = RPS2 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 EFQIIDTLLPGLQDEVMNIKPVX 0.4963 0.00439 0.4363 0.9932 1.18E+06 QK Hit Accession Score Mass L/(L+ H) SD (geo) # 127 P43620 39 75867 0.5908 1 RMD8_YEAST Sporulationprotein RMD8 OS = Saccharomyces cerevisiae GN = RMD8 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 REQLLK X 0.5908 0.00487 0.1874 0.9696 5.33E+05 HitAccession Score Mass L/(L + H) SD (geo) # 128 P52910 39 75765 0ACS2_YEAST Acetyl-coenzyme A synthetase 2 OS = Saccharomyces cerevisiaeGN = ACS2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 129 P60010 38 41663 0 ACT_YEAST Actin OS = Saccharomycescerevisiae GN = ACT1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 DLTDYLMK 0.8897 0.013240.1224 0.6466 4.23E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 130P41805 37 25522 0.7348 1 RL10_YEAST 60S ribosomal protein L10 OS= Saccharomyces cerevisiae GN = RPL10 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3WGFTNLDRPEYLK X 0.7348 0.02758 0.107 0.8056 2.97E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 131 Q86ZR7 37 26338 0 YKD3A_YEAST Putativeuncharacterized hydrolase YKL033W-A OS = Saccharomyces cerevisiae GN= YKL033W-A PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 132 P38205 35 77830 0 NCL1_YEAST tRNA(cytosine-5-)-methyltransferase NCL1 OS = Saccharomyces cerevisiae GN= NCL1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LSSETPALESEGPQTK 0.3404 0.019690.1416 0.3584 2.22E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 133P17255 35 118562 0 VATA_YEAST V-type proton ATPase catalytic subunit AOS = Saccharomyces cerevisiae GN = TFP1 PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3AIKEESQSIYIPR 0.2979 0.2188 0.09557 0.4074 1.46E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 134 P05739 35 20183 0.5423 1 RL6B_YEAST 60Sribosomal protein L6-B OS = Saccharomyces cerevisiae GN = RPL6B PE = 1SV = 4 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 HLEDNTLLVTGPFK X 0.5423 0.02668 0.22650.9184 1.35E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 135 Q0753035 34457 0.9709 1 YD114_YEAST Uncharacterized oxidoreductase YDL114W OS= Saccharomyces cerevisiae GN = YDL114W PE = 2 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2INRASGTTK X 0.9709 0.00996 0.1262 0.9924 1.27E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 136 P15625 34 57804 0 SYFA_YEASTPhenylalanyl-tRNA synthetase alpha chain OS = Saccharomyces cerevisiaeGN = FRS2 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 137 Q02209 33 41274 0.9909 1 YKZ1_YEAST Uncharacterizedprotein YKR011C OS = Saccharomyces cerevisiae GN = YKR011C PE = 1 SV = 2z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 FQLVEK X 0.9909 0.00329 0.1232 0.9948 5.97E+05 HitAccession Score Mass L/(L + H) SD (geo) # 138 A6ZZJ1 32 143286 0.5908 1MYO3_YEAS7 Myosin-3 OS = Saccharomyces cerevisiae (strain YJM789) GN= MYO3 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 RIDAAIK X 0.5908 0.00487 0.18740.9696 5.33E+05 2 3 IIKSANELVETLSK 0.5256 0.06512 0.2213 0.1936 2.39E+05Hit Accession Score Mass L/(L + H) SD (geo) # 139 P40077 32 64327 0DSE1_YEAST Protein DSE1 OS = Saccharomyces cerevisiae GN = DSE1 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 MNSPILRK 0.003135 3.635 0.06896 0.9784 7203Hit Accession Score Mass L/(L + H) SD (geo) # 140 A7A1S5 31 76547 0DUS3_YEAS7 tRNA-dihydrouridine synthase 3 OS = Saccharomyces cerevisiae(strain YJM789) GN = DUS3 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2 QNENQK 0.44680.05701 0.00365 0.6454 6837 Hit Accession Score Mass L/(L + H) SD (geo)# 141 P02557 31 51011 0 TBB_YEAST Tubulin beta chain OS = Saccharomycescerevisiae GN = TUB2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 142 P17423 31 38792 0 KHSE_YEAST Homoserine kinaseOS = Saccharomyces cerevisiae GN = THR1 PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 143 P04076 30 52173 0ARLY_YEAST Argininosuccinate lyase OS = Saccharomyces cerevisiae GN= ARG4 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 144 A6ZWD3 29 68204 0 DBP1_YEAS7 ATP-dependent RNA helicaseDBP1 OS = Saccharomyces cerevisiae (strain YJM789) GN = DBP1 PE = 3 SV= 1 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 145 P0770229 155248 0 LYS2_YEAST L-aminoadipate-semialdehyde dehydrogenase OS= Saccharomyces cerevisiae GN = LYS2 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2EYFVEPNSAEGK 0.0214 0.957 0.3831 0.02822 9.46E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 146 P39976 27 55190 0 DLD3_YEAST D-lactatedehydrogenase [cytochrome] 3 OS = Saccharomyces cerevisiae GN = DLD3 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 LNAAGLIGDAPKPVVK 1 0.00277 0.1741 0.29788.97E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 147 P53953 2798881 0.4536 1 SFB2_YEAST SED5-binding protein 2 OS = Saccharomycescerevisiae GN = SFB2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SEQGILNTPK X 0.45360.03249 0.3059 0.9489 4.80E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 148 Q08647 27 77419 0 PUS7_YEAST Multisubstrate pseudouridinesynthase 7 OS = Saccharomyces cerevisiae GN = PUS7 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 149 Q0779826 102104 0.9876 1 SPO75_YEAST Sporulation-specific protein 75 OS= Saccharomyces cerevisiae GN = SPO75 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2ILDKIIR X 0.9876 0.00489 0.02083 0.9895 5.42E+04 Hit Accession ScoreMass L/(L + H) SD (geo) # 150 P29509 26 34409 0.3208 1 TRXB1_YEASTThioredoxin reductase 1 OS = Saccharomyces cerevisiae GN = TRR1 PE = 1SV = 3 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 IVAGQVDTDEAGYIK X 0.3208 0.06408 0.42810.9649 5.48E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 151 P3872026 53774 0 6PGD1_YEAST 6-phosphogluconate dehydrogenase, decarboxylating1 OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 152 P26785 26 22444 0RL16B_YEAST 60S ribosomal protein L16-B OS = Saccharomyces cerevisiae GN= RPL16B PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 153 P06843 25 38928 0.5908 1 SPT2_YEAST Protein SPT2 OS= Saccharomyces cerevisiae GN = SPT2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 RQELLK X0.5908 0.00487 0.1874 0.9696 5.33E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 154 P06101 25 58845 0.9702 1 CDC37_YEAST Hsp90 co-chaperoneCdc37 OS = Saccharomyces cerevisiae GN = CDC37 PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 VFEDIPIEEAEK X 0.9702 0.01138 0.1397 0.737 1.27E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 155 P07149 25 228547 0 FAS1_YEAST Fattyacid synthase subunit beta OS = Saccharomyces cerevisiae GN = FAS1 PE= 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 WETTTQFK 0.3417 0.07701 0.06965 0.69645.87E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 156 P35169 24280962 1.001 1 TOR1_YEAST Serine/threonine-protein kinase TOR1 OS= Saccharomyces cerevisiae GN = TOR1 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 EIKFIK X1.001 0 0.1891 0.9934 1.08E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 157 Q05016 24 29301 0 YM71_YEAST Uncharacterized oxidoreductaseYMR226C OS = Saccharomyces cerevisiae GN = YMR226C PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 IKPFIENLPQEFK 0.4711 0.02328 0.1926 0.2766 5.31E+04Hit Accession Score Mass L/(L + H) SD (geo) # 158 P23796 24 59181 0RIT1_YEAST tRNA A64-2′-O-ribosylphosphate transferase OS = Saccharomycescerevisiae GN = RIT1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 LNELFMGK 0.173 0.15990.1023 0.6886 5.41E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 159Q12734 23 124772 0.9979 1 CSR2_YEAST Transcription factor CSR2 OS= Saccharomyces cerevisiae GN = CSR2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 STTLSDIKX 0.9979 0 0.5316 0.9992 3.05E+06 Hit Accession Score Mass L/(L + H) SD(geo) # 160 P24384 23 130674 0.5908 1 PRP22_YEAST Pre-mRNA-splicingfactor ATP-dependent RNA helicase PRP22 OS = Saccharomyces cerevisiae GN= PRP22 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 ERALGIK X 0.5908 0.00487 0.18740.9696 5.33E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 161 Q0441223 54780 0.9523 1 AGE1_YEAST ADP-ribosylation factor GTPase-activatingprotein effector protein 1 OS = Saccharomyces cerevisiae GN = AGE1 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 LTNILLK X 0.9523 0.00751 0.01207 0.90721.83E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 162 P53191 2270950 0 PIB2_YEAST Phosphatidylinositol-3-phosphate-binding protein 2 OS= Saccharomyces cerevisiae GN = PIB2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 163 Q03497 22 102940 1 1STE20_YEAST Serine/threonine-protein kinase STE20 OS = Saccharomycescerevisiae GN = STE20 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ETLSGLEFLHSK X 10.00609 0.6136 0.9975 1.27E+06 Hit Accession Score Mass L/(L + H) SD(geo) # 164 P40462 22 107655 0.9911 1 TM108_YEAST Protein TMA108 OS= Saccharomyces cerevisiae GN = TMA108 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2FINLEK X 0.9911 0.00377 0.122 0.9964 5.91E+05 Hit Accession Score MassL/(L + H) SD (geo) # 165 P05755 22 22285 0 RS9B_YEAST 40S ribosomalprotein S9-B OS = Saccharomyces cerevisiae GN = RPS9B PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 LDYVLALK 0.005702 1.64 0.079 0.8879 9978 Hit AccessionScore Mass L/(L + H) SD (geo) # 166 P46679 22 97766 0 STB2_YEAST ProteinSTB2 OS = Saccharomyces cerevisiae GN = STB2 PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 SSLQGQGKTGICSAIDPKSDK 0.9544 0.00932 0.1894 0.3151 7.47E+05 HitAccession Score Mass L/(L + H) SD (geo) # 167 P0C0W1 22 14705 0RS22A_YEAST 40S ribosomal protein S22-A OS = Saccharomyces cerevisiae GN= RPS22A PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 168 P36096 22 88064 0.9908 1 TUL1_YEAST Transmembrane E3ubiquitin-protein ligase 1 OS = Saccharomyces cerevisiae GN = TUL1 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 IDLVSNNK X 0.9908 0.00823 0.03719 0.97281.54E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 169 P38967 2165362 0 TAT2_YEAST Tryptophan permease OS = Saccharomyces cerevisiae GN= TAT2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 170 Q05955 21 57795 0.8578 1 ADY4_YEAST Accumulates dyadsprotein 4 OS = Saccharomyces cerevisiae GN = ADY4 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 DVDYQTFK X 0.8578 0.03111 0.08023 0.9212 1.78E+05 HitAccession Score Mass L/(L + H) SD (geo) # 171 P26786 21 21761 0RS7A_YEAST 40S ribosomal protein S7-A OS = Saccharomyces cerevisiae GN= RPS7A PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 172 P18759 21 84004 1 1 SEC18_YEAST Vesicular-fusion proteinSEC18 OS = Saccharomyces cerevisiae GN = SEC18 PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 FKIPGFGK X 1 0.00372 0.3628 0.9814 2.01E+05 Hit Accession Score MassL/(L + H) SD (geo) # 173 P02309 21 11361 0.4287 1 H4_YEAST Histone H4 OS= Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2DSVTYTEHAK X 0.4287 0.05722 0.06178 0.844 1.78E+04 Hit Accession ScoreMass L/(L + H) SD (geo) # 174 P36139 20 31428 0 PET10_YEAST ProteinPET10 OS = Saccharomyces cerevisiae GN = PET10 PE = 1 SV = 3 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 LDELVNLLVFK −0.001257 0.6587 0.7685 0.9993 1.17E+06 Hit AccessionScore Mass L/(L + H) SD (geo) # 175 Q02773 20 140029 1 RPM2_YEASTRibonuclease P protein component, mitochondrial OS = Saccharomycescerevisiae GN = RPM2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SLLRKSKPLQA X 0 9990.00047 0.8095 271.1 Hit Accession Score Mass L/(L + H) SD (geo) # 176P38697 20 56494 0.3128 1 IMDH2_YEAST Inosine-5′-monophosphatedehydrogenase IMD2 OS = Saccharomyces cerevisiae GN = IMD2 PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 TASAQLEGGVHNLHSYEK X 0.3128 0.09825 0.218 0.83061.40E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 177 P41832 20221017 0.02392 1 BNI1_YEAST Protein BNI1 OS = Saccharomyces cerevisiaeGN = BNI1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 RLKELETK X 0.02392 0.28880.00547 0.8577 1621 Hit Accession Score Mass L/(L + H) SD (geo) # 178P17119 20 83952 0.09389 1 KAR3_YEAST Kinesin-like protein KAR3 OS= Saccharomyces cerevisiae GN = KAR3 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 TNLETLEKX 0.09389 0.2254 0.0084 0.9135 5.14E+04 Hit Accession Score Mass L/(L+ H) SD (geo) # 179 P15303 20 85579 0 SEC23_YEAST Protein transportprotein SEC23 OS = Saccharomyces cerevisiae GN = SEC23 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 180 P3256520 104768 0 RPN2_YEAST 26S proteasome regulatory subunit RPN2 OS= Saccharomyces cerevisiae GN = RPN2 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 181 Q03660 20 128787 0TR130_YEAST Transport protein particle 130 kDa subunit OS= Saccharomyces cerevisiae GN = TRS130 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 182 P39081 19 71853 0PCF11_YEAST Protein PCF11 OS = Saccharomyces cerevisiae GN = PCF11 PE= 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 INNLYASLKAEGLIYTPPK 0.9323 0.01402 0.35410.6434 6.37E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 183 B3LRC219 36810 0 UTH1_YEAS1 Protein UTH1 OS = Saccharomyces cerevisiae (strainRM11-1a) GN = UTH1 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 184 P07259 19 244972 0 PYR1_YEAST Protein URA1 OS= Saccharomyces cerevisiae GN = URA2 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 185 P18963 19 350758 0.9999 1IRA1_YEAST Inhibitory regulator protein IRA1 OS = Saccharomycescerevisiae GN = IRA1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 GNKYLIK X 0.99990.00158 0.0893 0.9713 3.78E+04 Hit Accession Score Mass L/(L + H) SD(geo) # 186 P38850 18 123854 0 RT107_YEAST Regulator of Ty1transposition protein 107 OS = Saccharomyces cerevisiae GN = RTT107 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) #187 Q04199 18 51420 0 CAC2_YEAST Chromatin assembly factor 1 subunit p60OS = Saccharomyces cerevisiae GN = CAC2 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2IPCNSSDSK 0.9943 0.00328 0.1865 0.52 1.44E+06 Hit Accession Score MassL/(L + H) SD (geo) # 188 Q12345 17 28402 0 IES3_YEAST Ino eighty subunit3 OS = Saccharomyces cerevisiae GN = IES3 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3IDILTKIQENLLEEYQK 0.04155 1.417 0.06472 0.5595 1068 Hit Accession ScoreMass L/(L + H) SD (geo) # 189 P53598 17 35010 1.001 1 SUCA_YEASTSuccinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial OS= Saccharomyces cerevisiae GN = LSC1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 ESIPYDKX 1.001 0.001 0.6215 0.9959 3.11E+06

TABLE 2 Proteins identified by Mascot Distiller from ChAP-MS analysis ofGAL1 chromatin isolated from cells grown in galactose. Mascot DistillerQuantitation Report Mascot search results: Galactose Log ratio versusLog ratio versus Intensity (all Intensity (selected positive ratios)ratios) 0 2.00e+7 0 5.00e+6 4.00e+7 6.00e+7 1.00e+7 1.50e+7 −6 L/(L + H)−15 −10 −5 0 5 −4 −2 0 2 Hit Accession Score Mass L/(L + H) SD (geo) # 1P00924 952 46773 0.727 1.077 10 ENO1_YEAST Enolase 1 OS = Saccharomycescerevisiae GN = ENO1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 RIATAIEK X 0.9922 0.0010.0623 0.9937 78080.00 2 2 VNQIGTLSESIK X 0.7237 0.001 0.6107 0.99711.48E+06 3 3 AVDDFLISLDGTANK X 0.6953 0.00258 0.5605 0.9825 2.57E+05 4 2AVDDFLISLDGTANK X 0.678 0.00158 0.1606 0.9839 3.20E+06 5 2TAGIQIVADDLTVTNPK X 0.8499 0 0.4502 0.9983 8.74E+05 6 3IEEELGDNAVFAGENFHHGDK X 0.7139 0.01531 0.04418 0.7314 3.10E+04 7 2IEEELGDNAVFAGENFHHGDKL X 0.8709 0.00321 0.8165 0.9933 1.28E+05 8 3IEEELGDNAVFAGENFHHGDKL X 0.8482 0.00579 0.7751 0.9956 5.69E+05 9 3YPIVSIEDPFAEDDWEAWSHFFK X 0.743 0.001 0.7934 0.9984 1.74E+06 10  3RYPIVSIEDPFAEDDWEAWSHFFK 0.2589 0.1734 0.2248 0.5408  1353 11  3YGASAGNVGDEGGVAPNIQTAEE X 0.7223 0.00158 0.9201 0.9993 1.05E+07ALDLIVDAIK Hit Accession Score Mass L/(L + H) SD (geo) # 2 P00925 82746885 0.7156 1.024 5 ENO2_YEAST Enolase 2 OS = Saccharomyces cerevisiaeGN = ENO2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 VNQIGTLSESIK X 0.7237 0.0010.6107 0.9971 1.48E+06 2 3 AVDDFLLSLDGTANK X 0.6953 0.00258 0.56050.9825 2.57E+05 3 2 AVDDFLLSLDGTANK X 0.678 0.00158 0.1606 0.98393.20E+06 4 2 DGKYDLDFKNPESDK 0.593 0.03836 0.2515 0.6481 3.31E+05 5 3DGKYDLDFKNPESDK 0.2183 0.1283 0.2233 0.1889 8.04E+05 6 3YPIVSIEDPFAEDDWEAWSHFFK X 0.743 0.001 0.7934 0.9984 1.74E+06 7 3RYPIVSIEDPFAEDDWEAWSHFFK 0.2589 0.1734 0.2248 0.5408 1353 8 3YGASAGNVGDEGGVAPNIQTAEE X 0.7223 0.00158 0.9201 0.9993 1.05E+07ALDLIVDAIK Hit Accession Score Mass L/(L + H) SD (geo) # 3 P00359 77335724 0.6771 1.019 7 G3P3_YEAST Glyceraldehyde-3-phosphate dehydrogenase3 OS = Saccharomyces cerevisiae GN = TDH3 PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3ETTYDEIKK X 0.6838 0.00472 0.3538 0.9553 3.68E+05 2 2 TASGNIIPSSTGAAK X0.6648 0.00158 0.6513 0.9983 3.86E+06 3 2 VPTVDVSVVDLTVK X 0.7282 0.00640.2127 0.8286 6.60E+05 4 3 LNKETTYDEIKK 0.7548 0.04527 0.0313 0.20685.04E+04 5 3 YAGEVSHDDKHIIVDGK 0.688 0.0049 0.1652 0.6807 4.07E+06 6 2YAGEVSHDDKHIIVDGK X 0.6826 0.00224 0.3878 0.8652 2.07E+06 7 3KVVITAPSSTAPMFVMGVNEEK X 0.7193 0.00631 0.1023 0.9512 2.42E+05 8 2DPANLPWGSSNVDIAIDSTGVFK X 0.6776 0.00494 0.5179 0.9695 1.47E+06 9 3DPANLPWGSSNVDIAIDSTGVFK 0.6946 0.02605 0.3559 0.4268 1.47E+06 10  3VINDAFGIEEGLMTTVHSLTATQK X 0.6612 0.0114 0.3918 0.9512 5.69E+05 HitAccession Score Mass L/(L + H) SD (geo) # 4 P02994 662 50394 0.85041.012 7 EF1A_YEAST Elongation factor 1-alpha OS = Saccharomycescerevisiae GN = TEF1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 FDELLEK X 0.826 0.001580.3074 0.9923 4.71E+06 2 3 SHINVVVIGHVDSGK 0.8651 0.00919 0.1342 0.42491.91E+05 3 2 TLLEAIDAIEQPSRPTDKPLR X 0.8558 0 0.7243 0.9974 1.11E+06 4 3TLLEAIDAIEQPSRPTDKPLR X 0.8371 0.00322 0.6393 0.9893 8.82E+06 5 3VETGVIKPGMVVTFAPAGVTTEVK X 0.8774 0.001 0.7139 0.9992 6.53E+06 6 2VETGVIKPGMVVTFAPAGVTTEVK X 0.8911 0 0.7784 0.9982 2.27E+06 7 3SVEMHHEQLEQGVPGDNVGFNVK X 0.8474 0.00071 0.7764 0.9988 1.10E+07 8 2SVEMHHEQLEQGVPGDNVGFNVK X 0.8482 0.001 0.8709 0.999 1.09E+06 HitAccession Score Mass L/(L + H) SD (geo) # 5 P54115 486 54380 0.68811.024 5 ALDH6_YEAST Magnesium-activated aldehyde dehydrogenase,cytosolic OS = Saccharomyces cerevisiae GN = ALD6 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 SVAVDSSESNLK X 0.7081 0.0109 0.05156 0.971 5.45E+05 23 SVAVDSSESNLKK X 0.6272 0.01694 0.1014 0.9286 2.04E+05 3 2SVAVDSSESNLKK X 0.6886 0.00158 0.2331 0.997 7.45E+05 4 3 SAHLVFDDANIKK X0.6792 0.004 0.1402 0.9596 2.03E+05 5 3 IVKEEIFGPVVTVAK 0.2547 0.078490.4923 0.06903 3.53E+06 6 2 IVKEEIFGPVVTVAK X 0.6996 0.00158 0.18330.9947 3.23E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 6 P10591482 70039 0.8188 1.018 4 HSP71_YEAST Heat shock protein SSA1 OS= Saccharomyces cerevisiae GN = SSA1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2MKETAESYLGAK X 0.7735 0.00986 0.2692 0.9866 2.32E+05 2 2 NFNDPEVQADMK X0.8218 0.00856 0.2133 0.9657 9.80E+05 3 2 NQAAMNPSNTVFDAK X 0.81860.0035 0.4594 0.9975 1.37E+06 4 3 NTISEAGDKLEQADKDTVTK 0.3583 0.064910.4424 0.4808 1.01E+07 5 2 NTISEAGDKLEQADKDTVTK X 0.8301 0.00158 0.61570.995 7.24E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 7 P50095425 56813 0.9382 1.024 5 IMDH3_YEAST Probable inosine-5′-monophosphatedehydrogenase IMD3 OS = Saccharomyces cerevisiae GN = IMD3 PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 TASAQLEGGVHNLHSYEK 0.4222 0.1268 0.5294 0.31167.78E+05 2 2 TASAQLEGGVHNLHSYEK X 0.893 0.02366 0.2283 0.9113 2.44E+05 32 NPVTGAQGITLSEGNEILK X 0.9433 0.00754 0.3647 0.9924 1.01E+06 4 3NPVTGAQGITLSEGNEILK X 0.9335 0.00158 0.3228 0.9933 3.39E+05 5 2YFSESDSVLVAQGVSGAVVDK X 1 0.001 0.4121 0.9864 7.24E+04 6 2GGLTYNDFLVLPGLVDFPSSEVSL X 0.9534 0 0.8179 0.9932 2.35E+05 QTK HitAccession Score Mass L/(L + H) SD (geo) # 8 P07262 383 49539 0.56661.061 3 DHE4_YEAST NADP-specific glutamate dehydrogenase 1 OS= Saccharomyces cerevisiae GN = GDH1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2STATGPSEAVWYGPPK X 0.6132 0.00959 0.3565 0.9733 2.44E+05 2 3VTWENDKGEQEVAQGYR X 0.535 0.02836 0.5322 0.8087 5.75E+05 3 2VTWENDKGEQEVAQGYR X 0.6306 0.00328 0.4773 0.9937 1.29E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 9 P06169 369 61737 0.5627 5 PDC1_YEASTPyruvate decarboxylase isozyme 1 OS = Saccharomyces cerevisiae GN = PDC1PE = 1 SV = 7 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 VATTGEWDKLTQDK X 0.5604 0.00308 0.37820.9946 8.35E+05 2 3 YGGVYVGTLSKPEVK X 0.5512 0.00325 0.3138 0.98164.29E+05 3 2 YGGVYVGTLSKPEVK X 0.5578 0.001 0.3925 0.9961 8.00E+05 4 3LLQTPIDMSLKPNDAESEK X 0.6389 0.08423 0.3737 0.9119 2000 5 2MIEIMLPVFDAPQNLVEQAK X 0.6331 0.00453 0.5965 0.979 1.63E+05 HitAccession Score Mass L/(L + H) SD (geo) # 10 P29311 363 30209 0.77441.108 3 BMH1_YEAST Protein BMH1 OS = Saccharomyces cerevisiae GN = BMH1PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 QAFDDAIAELDTLSEESYK X 0.7998 0.00255 0.53950.9946 4.35E+05 2 2 ISDDILSVLDSHLIPSATTGESK X 0.625 0.01278 0.271 0.72831.76E+05 3 3 ISDDILSVLDSHLIPSATTGESK X 0.7868 0.00158 0.1746 0.99721.49E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 11 P15108 36181435 0.007455 6 HSC82_YEAST ATP-dependent molecular chaperone HSC82 OS= Saccharomyces cerevisiae GN = HSC82 PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2AILFIPK X 0.7304 0.00664 0.3427 0.9954 5.12E+04 2 2 RVDEGGAQDK X 0.7340.007 0.04224 0.965 9084 3 2 KDEDDKKPK 0.4443 0.1702 0.04474 0.339 22024 2 ALKDILGDQVEK X 0.7398 0.01231 0.03927 0.8976 8.40E+04 5 3VKEEVQELEELNK X 0.711 0.00306 0.1697 0.9942 2.85E+05 6 2 LEEVDEEEEEKKPKX 0.6241 0.03842 0.06528 0.873 2.25E+05 7 3 TLVDITKDFELEETDEEKAER X0.005607 0.09361 0.4759 0.9104 1.04E+07 Hit Accession Score Mass L/(L+ H) SD (geo) # 12 P46655 353 81369 0.8084 4 SYEC_YEAST Glutamyl-tRNAsynthetase, cytoplasmic OS = Saccharomyces cerevisiae GN = GUS1 PE = 1SV = 3 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 ANFEIDLPDAK X 0.8028 0.00578 0.1682 0.97436.26E+05 2 2 IHLEGSEAPQEPK X 0.8001 0.01046 0.2506 0.9636 5.39E+05 3 3EKEEFQDSILEDLDLLGIK X 0.8258 0.00576 0.2679 0.9657 5.87E+05 4 2EKEEFQDSILEDLDLLGIK X 0.7985 0.00441 0.3707 0.9948 1.96E+05 HitAccession Score Mass L/(L + H) SD (geo) # 13 P32589 346 77318 0.73181.014 3 HSP7F_YEAST Heat shock protein homolog SSE1 OS = Saccharomycescerevisiae GN = SSE1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 EELEELVKPLLER X 0.75360.03052 0.07918 0.8999 7.17E+04 2 2 GKLEEEYAPFASDAEK 0.6193 0.016230.1684 0.5929 1.11E+06 3 2 IIGLDYHHPDFEQESK X 0.7328 0.01091 0.085470.9763 8.03E+04 4 3 QVEDEDHMEVFPAGSSF X 0.7218 0.01002 0.3701 0.88891.59E+05 PSTK Hit Accession Score Mass L/(L + H) SD (geo) # 14 P00560322 44711 0.5639 1.448 3 PGK_YEAST Phosphoglycerate kinase OS= Saccharomyces cerevisiae GN = PGK1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2VDFNVPLDGK X 0.272 0.04331 0.3024 0.8665 1.97E+06 2 2 VLENTEIGDSIFDK0.9987 0 0.8558 0.2984 5.35E+07 3 2 SSAAGNTVIIGGGDTATV X 0.7606 0.008380.6009 0.9775 2.98E+06 AK 4 2 GVEVVLPVDFIIADAFSAD X 0.8169 0.002710.6174 0.9986 1.47E+06 ANTK Hit Accession Score Mass L/(L + H) SD (geo)# 15 P00549 296 54807 0.7976 1.025 5 KPYK1_YEAST Pyruvate kinase 1 OS= Saccharomyces cerevisiae GN = PYK1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3MNFSHGSYEYHK X 0.7461 0.02847 0.1614 0.8404 2.71E+05 2 2 MNFSHGSYEYHK X0.8117 0.00999 0.1068 0.9731 4.19E+05 3 2 GVNLPGTDVDLPALSEK X 0.80430.00272 0.5459 0.9882 6.30E+06 4 2 GDLGIEIPAPEVLAVQK X 0.7994 0.0010.5602 0.9987 7.61E+06 5 2 SEELYPGRPLAIALDTK 0.002097 3.304 0.12910.6758 1.89E+05 6 3 KSEELYPGRPLAIALDTK X 0.7575 0.00877 0.1331 0.79721.12E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 16 P38720 29553509 0.9328 1.029 4 6PGD1_YEAST 6-phosphogluconate dehydrogenase,decarboxylating 1 OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 SIIGATSIEDFISK X 0.9129 0.001 0.1873 0.9973 1.68E+05 23 LGGFTDKEISDVFAK X 0.949 0.00158 0.2086 0.9846 6.26E+05 3 2AYREEPDLENLLFNK X 0.936 0.00484 0.3345 0.723 3.06E+06 4 3YGPSLMPGGSEEAWPHIK X 0.8712 0.00561 0.3785 0.9595 2.62E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 17 P04385 290 57907 0.6139 1.13 4GAL1_YEAST Galactokinase OS = Saccharomyces cerevisiae GN = GAL1 PE = 1SV = 4 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 NPSITLINADPK X 0.7365 0.001 0.5381 0.99532.36E+06 2 3 MLVLVEESLANKK X 0.7882 0.0105 0.2982 0.9203 2.53E+05 3 2SHSEEVIVPEFNSSAK X 0.5377 0.04126 0.3609 0.9033 3.79E+06 4 2VLNEKNPSITLINADPK X 0.7577 0.00342 0.1352 0.9951 4.28E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 18 P04397 264 78146 0.6778 7 GAL10_YEASTBifunctional protein GAL10 OS = Saccharomyces cerevisiae GN = GAL10 PE= 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 1 LEVLTK X 0.8734 0.001 0.01287 0.99369.32E+04 2 2 DYIHVVDLAK X 0.8614 0.00158 0.2342 0.9952 1.38E+06 3 3DYIHVVDLAK X 0.9574 0 0.4691 0.9578 4.66E+05 4 2 AGDVLNLTAKPDR X 0.80880.00531 0.07739 0.9941 4.67E+05 5 2 EIATFNSTKPTVLGPK X 1.003 0.011040.02312 0.9843 1.39E+04 6 2 YAIENILNDLYNSDK X 0.5331 0.02963 0.36560.7372 2.83E+06 7 2 SVDVDKNMIPTGNIVDR X 0.8696 0.00158 0.2804 0.99563.03E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 19 P11484 26266561 0.8176 1.003 3 HSP75_YEAST Heat shock protein SSB1 OS= Saccharomyces cerevisiae GN = SSB1 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2LLSDFFDGK X 0.8188 0.001 0.534 0.998 9.62E+05 2 2 RFDDESVQK X 0.82120.00341 0.3458 0.9841 1.10E+06 3 2 ENTLLGEFDLK X 0.8144 0.00158 0.40740.9981 1.59E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 20 P08431261 42358 0.6343 8.653 3 GAL7_YEAST Galactose-1-phosphateuridylyltransferase OS = Saccharomyces cerevisiae GN = GAL7 PE = 1 SV= 4 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 EHNTDLFADYVK X 0.01158 0.4988 0.2836 0.9602 5.87E+05 22 LDQPILPQNDSNEDNLK X 0.918 0 0.8548 0.9997 6.17E+06 3 3RPWLGQQEAAYKPTAPL X 0.7836 0.01208 0.1133 0.9209 3.76E+05 YDPK HitAccession Score Mass L/(L + H) SD (geo) # 21 Q01560 247 45444 0NOP3_YEAST Nucleolar protein 3 OS = Saccharomyces cerevisiae GN = NPL3PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) # 22P07284 238 53677 0.2383 4 SYSC_YEAST Seryl-tRNA synthetase, cytoplasmicOS = Saccharomyces cerevisiae GN = SES1 PE = 1 SV = 2 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2YIPGEPEFLPFVNELPK X 0.8227 0.00158 0.4653 0.9473 1.11E+05 2 3NASVEIVDEIISDYKDWVK X 0.7951 0.00573 0.4831 0.9887 3.44E+05 3 2NASVEIVDEIISDYKDWVK X 0.7696 0.01392 0.1984 0.9426 6.67E+04 4 3IEQFVITEPEKSWEEFEK X 0.114 0.1522 0.1374 0.9075 8.56E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 23 P38088 234 75364 0.8224 1.006 2SYG_YEAST Glycyl-tRNA synthetase 1 OS = Saccharomyces cerevisiae GN= GRS1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 IDDSGVSIGK X 0.8259 0.011710.1781 0.9752 4.43E+05 2 2 LDDDVVKEYEEILAK X 0.8161 0.01051 0.078470.9658 2.44E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 24 P17709225 55342 0.1024 15.72 2 HXKG_YEAST Glucokinase-1 OS = Saccharomycescerevisiae GN = GLK1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 EGHTLASDK X 0.0038440.1695 0.7656 0.9015 6.01E+05 2 2 YDVVIDQK X 0.836 0.0107 0.2711 0.96499.39E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 25 P10592 22369844 0.6324 1.099 3 HSP72_YEAST Heat shock protein SSA2 OS= Saccharomyces cerevisiae GN = SSA2 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2MKETAESYLGAK X 0.7735 0.00986 0.2692 0.9866 2.32E+05 2 2 NFNDPEVQGDMK X0.5921 0.01773 0.3417 0.9151 3.96E+05 3 3 NTISEAGDKLEQADKDAV X 0.61790.00324 0.3113 0.9818 8.87E+05 TK Hit Accession Score Mass L/(L + H) SD(geo) # 26 P34760 203 21688 0.8525 1 TSA1_YEAST Peroxiredoxin TSA1 OS= Saccharomyces cerevisiae GN = TSA1 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2TAVVDGVFDEVSLDK X 0.8525 0.003 0.2304 0.9765 1.37E+06 Hit AccessionScore Mass L/(L + H) SD (geo) # 27 P07806 202 126596 0.902 1.08 2SYV_YEAST Valyl-tRNA synthetase, mitochondrial OS = Saccharomycescerevisiae GN = VAS1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 TAEDQKDSIVSLIK X 0.82450.0142 0.06813 0.9834 6.02E+04 2 2 TGEVIINPLKEDGSPK X 0.9585 0.027480.09926 0.894 8.93E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 28P39015 200 29977 0.8734 1.037 2 STM1_YEAST Suppressor protein STM1 OS= Saccharomyces cerevisiae GN = STM1 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3TAQLSLQDYLNQQANNQ X 0.9037 0.0159 0.345 0.8549 1.14E+05 FNK 2 2EAQADAAAEIAEDAAEAE X 0.8405 0.03245 0.2666 0.956 1.01E+05 DAGKPK HitAccession Score Mass L/(L + H) SD (geo) # 29 P14540 196 39596 0.73781.02 2 ALF_YEAST Fructose-bisphosphate aldolase OS = Saccharomycescerevisiae GN = FBA1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 GISNEGQNASIK X 0.72320.00563 0.2971 0.9957 2.70E+06 2 2 LLPWFDGMLEADEAYFK X 0.7527 0.007010.6657 0.9971 2.69E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 30P07259 183 245990 0.6064 1 PYR1_YEAST Protein URA1 OS = Saccharomycescerevisiae GN = URA2 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SISGPVITDVASLK X 0.60640.03681 0.07372 0.792 2.43E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 31 P16521 177 115920 0.7059 1.311 3 EF3A_YEAST Elongation factor3A OS = Saccharomyces cerevisiae GN = YEF3 PE = 1 SV = 3 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 TQLRLKR X 0.9013 0.00444 0.3845 0.99 2.38E+06 2 2 AYEELSNTDLEFK X0.7997 0.02628 0.5649 0.9771 1.97E+06 3 3 AYEELSNTDLEFKFPEPG X 0.38630.03175 0.257 0.8484 1.37E+06 YLEGVK Hit Accession Score Mass L/(L + H)SD (geo) # 32 P11412 168 57830 0.5867 1.242 2 G6PD_YEASTGlucose-6-phosphate 1-dehydrogenase OS = Saccharomyces cerevisiae GN= ZWF1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 AVAPIDTDDVLLGQYGK X 0.56290.04227 0.2849 0.9375 7.08E+05 2 3 SEDGSKPAYVDDDTVDK X 0.7949 0.008560.1299 0.9748 9.45E+04 DSK Hit Accession Score Mass L/(L + H) SD (geo) #33 P07149 160 228547 0.8094 1 FAS1_YEAST Fatty acid synthase subunitbeta OS = Saccharomyces cerevisiae GN = FAS1 PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 GNYTDFENTFQK X 0.8094 0.01799 0.0845 0.9521 3.39E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 34 P28240 159 62369 0.3227 1 ACEA_YEASTIsocitrate lyase OS = Saccharomyces cerevisiae GN = ICL1 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 LDADAAEIEK X 0.3227 0.07711 0.202 0.9617 8.83E+05 HitAccession Score Mass L/(L + H) SD (geo) # 35 P00330 155 36800 0.86641.009 3 ADH1_YEAST Alcohol dehydrogenase 1 OS = Saccharomyces cerevisiaeGN = ADH1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 VVGLSTLPEIYEK X 0.8678 0.001580.5758 0.9962 2.12E+06 2 2 VLGIDGGEGKEELFR X 0.8513 0.00158 0.397 0.99772.05E+06 3 3 VLGIDGGEGKEELFR X 0.8778 0.00344 0.5496 0.9935 2.51E+06 HitAccession Score Mass L/(L + H) SD (geo) # 36 P32527 155 48990 0.8655 1ZUO1_YEAST Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 ATTIDEQVGLIVDSLNDEE X 0.8655 0.00448 0.4525 0.96132.75E+05 LVSTADK Hit Accession Score Mass L/(L + H) SD (geo) # 37 P04806155 53705 0.8304 1 HXKA_YEAST Hexokinase-1 OS = Saccharomyces cerevisiaeGN = HXK1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LSGNHTFDTTQSK 0.1191 0.2090.1488 0.6634 3.26E+05 2 3 TKYDVAVDEQSPRPGQQ X 0.8304 0.01169 0.13920.9589 2.37E+04 AFEK Hit Accession Score Mass L/(L + H) SD (geo) # 38P05750 153 26486 0.7359 1 RS3_YEAST 40S ribosomal protein S3 OS= Saccharomyces cerevisiae GN = RPS3 PE = 1 SV = 5 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3ALPDAVTIIEPKEEEPILAP X 0.7359 0.01251 0.06703 0.9895 3.55E+05 SVK HitAccession Score Mass L/(L + H) SD (geo) # 39 P53252 152 38486 0.8196 1PIL1_YEAST Sphingolipid long chain base-responsive protein PIL1 OS= Saccharomyces cerevisiae GN = PIL1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2APTASQLQNPPPPPSTTK X 0.8196 0.01915 0.2011 0.9301 1.74E+05 2 3ALLELLDDSPVTPGETRP 0.6536 0.03193 0.2367 0.6395 5.49E+05 AYDGYEASK HitAccession Score Mass L/(L + H) SD (geo) # 40 P00817 151 32280 0.467 4IPYR_YEAST Inorganic pyrophosphatase OS = Saccharomyces cerevisiae GN= IPP1 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LNDIEDVEK X 0.3227 0.07711 0.2020.9617 8.83E+05 2 3 LEITKEETLNPIIQDTK X 0.736 0.01106 0.2893 0.93144.97E+05 3 3 AVGDNDPIDVLEIGETIAY X 0.7062 0.00365 0.6552 0.992 1.59E+05TGQVK 4 2 AVGDNDPIDVLEIGETIAY X 0.741 0.002 0.7827 0.9921 7.42E+04 TGQVKHit Accession Score Mass L/(L + H) SD (geo) # 41 Q03048 144 15891 0COFI_YEAST Cofilin OS = Saccharomyces cerevisiae GN = COF1 PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 SGVAVADESLTAFNDLK 0.519 0.05769 0.1215 0.5982 3.04E+05Hit Accession Score Mass L/(L + H) SD (geo) # 42 P32324 142 93230 0.70583 EF2_YEAST Elongation factor 2 OS = Saccharomyces cerevisiae GN = EFT1PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 3 WTNKDTDAEGKPLER X 0.7908 0.00868 0.070430.8558 2.83E+05 2 2 WTNKDTDAEGKPLER X 0.1675 0.2545 0.2121 0.76222.57E+05 3 3 GQVVSEEQRPGTPLFTVK X 0.8025 0.001 0.5728 0.9927 2.98E+06Hit Accession Score Mass L/(L + H) SD (geo) # 43 A6ZP47 141 65697 0DED1_YEAS7 ATP-dependent RNA helicase DED1 OS = Saccharomyces cerevisiae(strain YJM789) GN = DED1 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2DVPEPITEFTSPPLDGLLL −0.00021 5.488 0.7663 0.08765 2.92E+06 ENIK HitAccession Score Mass L/(L + H) SD (geo) # 44 P22515 139 114195 0.756 1UBA1_YEAST Ubiquitin-activating enzyme E1 1 OS = Saccharomycescerevisiae GN = UBA1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SDDSNSKPNVDEYK X 0.7560.02454 0.07431 0.9725 4.83E+04 2 2 QFMYFDSLESLPDPK 0.000528 7.2960.0675 0.6501 1.43E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 45P38701 137 14011 0.6173 1 RS20_YEAST 40S ribosomal protein S20 OS= Saccharomyces cerevisiae GN = RPS20 PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2EKVEEQEQQQQQIIK X 0.6173 0.00734 0.2134 0.9546 6.58E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 46 P14742 133 80357 0 GFA1_YEASTGlucosamine--fructose-6-phosphate aminotransferase [isomerizing] OS= Saccharomyces cerevisiae GN = GFA1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 47 P22768 133 47175 0ASSY_YEAST Argininosuccinate synthase OS = Saccharomyces cerevisiae GN= ARG1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 48 P10664 131 39325 0.7018 1.054 3 RL4A_YEAST 60S ribosomalprotein L4-A OS = Saccharomyces cerevisiae GN = RPL4A PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 IPEIPLVVSTDLESIQK X 0.7524 0.00693 0.3528 0.93853.17E+05 2 2 IPEIPLVVSTDLESIQK X 0.6885 0.00408 0.4963 0.9979 7.46E+05 33 IINSSEIQSAIRPAGQATQK X 0.6478 0.00324 0.4073 0.9947 9.65E+04 HitAccession Score Mass L/(L + H) SD (geo) # 49 P35691 128 18849 0.8547 1TCTP_YEAST Translationally-controlled tumor protein homolog OS= Saccharomyces cerevisiae GN = TMA19 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2DIFSNDELLSDAYDAK X 0.8547 0.00941 0.2439 0.9901 9.80E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 50 P15303 127 85331 0 SEC23_YEASTProtein transport protein SEC23 OS = Saccharomyces cerevisiae GN = SEC23PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 FFLPLEQVEFK 0.7553 0.01157 0.2147 0.51911.45E+05 2 2 KAGYQDDPQYADFK 0.9927 0.02465 0.1877 0.3964 5.07E+04 HitAccession Score Mass L/(L + H) SD (geo) # 51 Q03690 124 145076 0.5813 1TIF31_YEAST Protein TIF31 OS = Saccharomyces cerevisiae GN = TIF31 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 DANTGEEVTEDFVNDINVK X 0.5813 0.0468 0.10580.8113 3.64E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 52 P04807117 54189 0.7785 1.004 2 HXKB_YEAST Hexokinase-2 OS = Saccharomycescerevisiae GN = HXK2 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ELMQQIENFEK X 0.78020.01438 0.2465 0.9009 7.27E+05 2 3 GFDIPNIENHDVVPMLQK X 0.7742 0.016870.1579 0.835 2.97E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 53P43545 115 31998 0.06161 1 SNZ3_YEAST Probable pyridoxine biosynthesisprotein SNZ3 OS = Saccharomyces cerevisiae GN = SNZ3 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 TKGEAGTGDVSEAVK X 0.06161 0.5232 0.2013 0.789 4.12E+05Hit Accession Score Mass L/(L + H) SD (geo) # 54 P17536 115 23527 0.31921 TPM1_YEAST Tropomyosin-1 OS = Saccharomyces cerevisiae GN = TPM1 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 KNQQLEEDLEESDTK X 0.3192 0.1604 0.088580.7363 1.43E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 55 P07264112 85741 0 LEUC_YEAST 3-isopropylmalate dehydratase OS = Saccharomycescerevisiae GN = LEU1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 EFEYKDQDQSSPK 0.3020.09083 0.02215 0.6239 1.86E+05 2 3 DDQGKDQETDFVLNVEP 0.5589 0.018610.2447 0.6753 2.83E+06 WR 3 2 DDQGKDQETDFVLNVEP 0.8426 0.002 0.72650.4088 5.60E+05 WR Hit Accession Score Mass L/(L + H) SD (geo) # 56P05744 110 12219 0.6213 1 RL33A_YEAST 60S ribosomal protein L33-A OS= Saccharomyces cerevisiae GN = RPL33A PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2IEGVATPQDAQFYLGK X 0.6213 0.0083 0.1734 0.995 1.38E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 57 P36008 110 46491 0.8109 1 EF1G2_YEASTElongation factor 1-gamma 2 OS = Saccharomyces cerevisiae GN = TEF4 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 GQDFAPAFDVAPDWESY X 0.8109 0.01799 0.34550.9756 2.24E+05 EYTK Hit Accession Score Mass L/(L + H) SD (geo) # 58P16862 108 104953 0.8294 1.029 2 K6PF2_YEAST 6-phosphofructokinasesubunit beta OS = Saccharomyces cerevisiae GN = PFK2 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 SSPDENSTLLSNDSISLK X 0.8127 0.01294 0.187 0.93531.95E+05 2 3 AAEENFNADDKTISDTAA X 0.8594 0.01841 0.2622 0.9073 1.12E+05VVGVK Hit Accession Score Mass L/(L + H) SD (geo) # 59 P11154 107 1305390.9707 1 PYC1_YEAST Pyruvate carboxylase 1 OS = Saccharomyces cerevisiaeGN = PYC1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 SFLSPLETDEEIEVVIEQGK X 0.97070.00158 0.4859 0.886 1.52E+06 2 3 EVFVSDGENVDSSDLLVL 0.5025 0.071150.1391 0.5886 1.13E+05 LEDQVPVETK Hit Accession Score Mass L/(L + H) SD(geo) # 60 P52910 106 75765 0 ACS2_YEAST Acetyl-coenzyme A synthetase 2OS = Saccharomyces cerevisiae GN = ACS2 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2TGTEGIPMK 0.6962 0.01855 0.4457 0.1173 7.72E+06 Hit Accession Score MassL/(L + H) SD (geo) # 61 P35844 106 49461 0.7224 1 KES1_YEAST ProteinKES1 OS = Saccharomyces cerevisiae GN = KES1 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 NAPSGTLVGDKEDR X 0.7224 0.06623 0.06821 0.8339 1.10E+05 2 3DFDYSVTPEEGALVPEKD 0.6484 0.09516 0.283 0.6012 1.42E+05 DTFLK HitAccession Score Mass L/(L + H) SD (geo) # 62 P36010 105 17268 0NDK_YEAST Nucleoside diphosphate kinase OS = Saccharomyces cerevisiae GN= YNK1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 TFIAVKPDGVQR 0.03719 0.71490.1927 0.2162 1.95E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 63P04802 104 63861 0.8286 1 SYDC_YEAST Aspartyl-tRNA synthetase,cytoplasmic OS = Saccharomyces cerevisiae GN = DPS1 PE = 1 SV = 3 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 EIGDFEDLSTENEK X 0.8286 0.00835 0.2225 0.9736 4.26E+05Hit Accession Score Mass L/(L + H) SD (geo) # 64 P12709 104 61582 0.77091.002 2 G6PI_YEAST Glucose-6-phosphate isomerase OS = Saccharomycescerevisiae GN = PGI1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 ANKPMYVDGVNVAPEVD X0.7705 0.01145 0.2097 0.7988 5.44E+05 SVLK 2 2 ANKPMYVDGVNVAPEVD X0.7726 0.02338 0.1041 0.9243 1.51E+05 SVLK Hit Accession Score Mass L/(L+ H) SD (geo) # 65 P15019 104 37302 0.8418 1.446 2 TAL1_YEASTTransaldolase OS = Saccharomyces cerevisiae GN = TAL1 PE = 1 SV = 4 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 DYKGEADPGVISVK X 0.9932 0.01166 0.08304 0.98743.01E+05 2 2 NLAGVDYLTISPALLDK X 0.5131 0.1041 0.121 0.9331 6.69E+04 HitAccession Score Mass L/(L + H) SD (geo) # 66 P14120 103 11504 0.6528 1RL30_YEAST 60S ribosomal protein L30 OS = Saccharomyces cerevisiae GN= RPL30 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 VYYFQGGNNELGTAVGK X 0.65280.01167 0.1559 0.9767 1.26E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 67 P22943 102 11806 0 HSP12_YEAST 12 kDa heat shock protein OS= Saccharomyces cerevisiae GN = HSP12 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 68 P0C2I7 101 199542 0.86241.013 2 YL14B_YEAST Transposon Ty1-LR4 Gag-Pol polyprotein OS= Saccharomyces cerevisiae GN = TY1B-LR4 PE = 3 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2DILSVDYTDIMK X 0.8498 0.02246 0.04882 0.8124 1.27E+05 2 2EVHTNQDPLDVSASK X 0.8722 0.01118 0.2043 0.9837 1.65E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 69 P0C2I5 101 198422 0.8624 1.013 2YL12B_YEAST Transposon Ty1-LR2 Gag-Pol polyprotein OS = Saccharomycescerevisiae GN = TY1B-LR2 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2 DILSVDYTDIMK X0.8498 0.02246 0.04882 0.8124 1.27E+05 2 2 EVHTNQDPLDVSASK X 0.87220.01118 0.2043 0.9837 1.65E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 70 P32598 101 35884 0.8363 1 PP12_YEAST Serine/threonine-proteinphosphatase PP1-2 OS = Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 GSKPGQQVDLEENEIR X 0.8363 0.01279 0.1472 0.98744.79E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 71 P25087 9943403 0.8036 1 ERG6_YEAST Sterol 24-C-methyltransferase OS= Saccharomyces cerevisiae GN = ERG6 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2KPENAETPSQTSQEATQ X 0.8036 0.04785 0.08929 0.8981 4.04E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 72 P08524 98 40458 0 FPPS_YEAST Farnesylpyrophosphate synthase OS = Saccharomyces cerevisiae GN = FPP1 PE = 1 SV= 2 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 IEQLYHEYEESIAK 0.3329 0.09842 0.4172 0.2092 1.03E+06Hit Accession Score Mass L/(L + H) SD (geo) # 73 P15705 97 66224 0STI1_YEAST Heat shock protein STI1 OS = Saccharomyces cerevisiae GN= STI1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 74 P25694 97 92331 0.8407 1 CDC48_YEAST Cell division controlprotein 48 OS = Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 NAPAIIFIDEIDSIAPK X 0.8407 0.0034 0.1098 0.99688.16E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 75 P00942 9626947 0.9321 1 TPIS_YEAST Triosephosphate isomerase OS = Saccharomycescerevisiae GN = TPI1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ASGAFTGENSVDQIK X0.9321 0.00579 0.6559 0.9989 1.71E+06 Hit Accession Score Mass L/(L + H)SD (geo) # 76 P02400 95 11099 0 RLA4_YEAST 60S acidic ribosomal proteinP2-beta OS = Saccharomyces cerevisiae GN = RPP2B PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 77 P40069 94122525 0 IMB4_YEAST Importin subunit beta-4 OS = Saccharomycescerevisiae GN = KAP123 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications Hit Accession ScoreMass L/(L + H) SD (geo) # 78 P32481 93 57829 0.8691 1.017 2 IF2G_YEASTEukaryotic translation initiation factor 2 subunit gamma OS= Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3LGDEIEIRPGIVTK 0.9246 0.04186 0.2121 0.3448 9.63E+04 2 3VAFTGLEEDGETEEEKR X 0.888 0.00751 0.1402 0.8705 2.90E+05 3 2EFEEGGGLPEQPLNPDF X 0.8595 0.00652 0.4126 0.9885 5.61E+05 SK HitAccession Score Mass L/(L + H) SD (geo) # 79 Q12230 92 38048 0.8619 1LSP1_YEAST Sphingolipid long chain base-responsive protein LSP1 OS= Saccharomyces cerevisiae GN = LSP1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2APTAAELQAPPPPPSSTK X 0.8619 0.03102 0.1585 0.8149 4.28E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 80 P0C0W9 90 19707 0 RL11A_YEAST 60Sribosomal protein L11-A OS = Saccharomyces cerevisiae GN = RPL11A PE = 1SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 VLEQLSGQTPVQSK 0.007131 0.04219 0.74020.3062 5.33E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 81 P3878886 58515 0 SSZ1_YEAST Ribosome-associated complex subunit SSZ1 OS= Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 82 P41811 85 99383 0COPB2_YEAST Coatomer subunit beta′ OS = Saccharomyces cerevisiae GN= SEC27 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 GEIEEAIENVLPNVEGK 0.473 0.099430.113 0.5911 1.71E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 83P38707 85 62168 0 SYNC_YEAST Asparaginyl-tRNA synthetase, cytoplasmic OS= Saccharomyces cerevisiae GN = DED81 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2SVQYVLEDPIAGPLVK 0.5764 0.02059 0.2109 0.4796 4.80E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 84 P00899 85 56732 0 TRPE_YEASTAnthranilate synthase component 1 OS = Saccharomyces cerevisiae GN= TRP2 PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 ESFLLESAK 0.9519 0.00995 0.24930.2379 2.91E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 85 P0C2H683 15522 0.6874 1 RL27A_YEAST 60S ribosomal protein L27-A OS= Saccharomyces cerevisiae GN = RPL27A PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2NQWFFSK 0.618 0.04071 0.1012 0.5142 1.00E+05 2 2 YTLDVEAFK X 0.68740.04111 0.01567 0.7996 2.90E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 86 P26321 83 33890 0 RL5_YEAST 60S ribosomal protein L5 OS= Saccharomyces cerevisiae GN = RPL5 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 87 P38115 83 38859 0.118 1ARA1_YEAST D-arabinose dehydrogenase [NAD(P)+] heavy chain OS= Saccharomyces cerevisiae GN = ARA1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2TMYAADGDYLETYK X 0.118 0.1798 0.2653 0.8455 1.50E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 88 P32599 82 72057 0 FIMB_YEAST Fimbrin OS= Saccharomyces cerevisiae GN = SAC6 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 89 A6ZXP4 81 50248 0.3547 1SUB2_YEAS7 ATP-dependent RNA helicase SUB2 OS = Saccharomyces cerevisiae(strain YJM789) GN = SUB2 PE = 3 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2 FLQNPLEIFVDDEAK X0.3547 0.08683 0.2049 0.8314 2.82E+04 Hit Accession Score Mass L/(L + H)SD (geo) # 90 P28273 80 140340 0 YKV5_YEAST Uncharacterized proteinYKL215C OS = Saccharomyces cerevisiae GN = YKL215C PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 91 P15625 8057804 0.7091 1 SYFA_YEAST Phenylalanyl-tRNA synthetase alpha chain OS= Saccharomyces cerevisiae GN = FRS2 PE = 1 SV = 3 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3DLQDTFYIKDPLTADLPD X 0.7091 0.04609 0.1531 0.7641 1.01E+05 DK HitAccession Score Mass L/(L + H) SD (geo) # 92 P38934 80 54606 0.2713 1BFR1_YEAST Nuclear segregation protein BFR1 OS = Saccharomycescerevisiae GN = BFR1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 INEIEESIASGDLSLVQEK X0.2713 0.04844 0.1734 0.8316 7.51E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 93 P05317 78 33866 0.9997 1 RLA0_YEAST 60S acidic ribosomalprotein P0 OS = Saccharomyces cerevisiae GN = RPP0 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 GTIEIVSDVK X 0.9997 0 0.5768 0.9991 4.62E+06 HitAccession Score Mass L/(L + H) SD (geo) # 94 P07257 78 40702 0QCR2_YEAST Cytochrome b-c1 complex subunit 2, mitochondrial OS= Saccharomyces cerevisiae GN = QCR2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 95 P46367 77 56688 0.916 1ALDH4_YEAST Potassium-activated aldehyde dehydrogenase, mitochondrial OS= Saccharomyces cerevisiae GN = ALD4 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2IAPALVTGNTVVLK X 0.916 0.00158 0.04226 0.9968 5.28E+04 Hit AccessionScore Mass L/(L + H) SD (geo) # 96 P16140 77 57713 0.5186 1 VATB_YEASTV-type proton ATPase subunit B OS = Saccharomyces cerevisiae GN = VMA2PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 AIVQVFEGTSGIDVK X 0.5186 0.06922 0.038560.8934 1.27E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 97 P3970874 49596 0.9962 1 DHE5_YEAST NADP-specific glutamate dehydrogenase 2 OS= Saccharomyces cerevisiae GN = GDH3 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3HIGKDTDVPAGDIGVGGR X 0.9962 0.0039 0.09871 0.9621 8.21E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 98 P15992 74 23865 0 HSP26_YEAST Heatshock protein 26 OS = Saccharomyces cerevisiae GN = HSP26 PE = 1 SV = 3z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 VITLPDYPGVDADNIK 0.1164 0.2258 0.295 0.3292 2.05E+05Hit Accession Score Mass L/(L + H) SD (geo) # 99 B3LP78 73 55768 0BLH1_YEAS1 Cysteine proteinase 1, mitochondrial OS = Saccharomycescerevisiae (strain RM11-1a) GN = LAP3 PE = 3 SV = 2 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 100 P32327 73 130638 0.62393.892 2 PYC2_YEAST Pyruvate carboxylase 2 OS = Saccharomyces cerevisiaeGN = PYC2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 NFLAPAEPDEEIEVTIEQ X 0.8940.01442 0.2074 0.9142 9.25E+05 GK 2 3 DGESVDASDLLVVLEEE X 0.09446 0.16070.3531 0.8345 1.76E+05 TLPPSQK Hit Accession Score Mass L/(L + H) SD(geo) # 101 P37291 73 52186 0 GLYC_YEAST Serinehydroxymethyltransferase, cytosolic OS = Saccharomyces cerevisiae GN= SHM2 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 LITSHLVDTDPEVDSIIKD 0.69450.07766 0.1892 0.388 1.35E+05 EIER Hit Accession Score Mass L/(L + H) SD(geo) # 102 P60010 73 41663 0.8046 1 ACT_YEAST Actin OS = Saccharomycescerevisiae GN = ACT1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 QEYDESGPSIVHHK 0.6740.07934 0.1333 0.5876 6.38E+04 2 2 QEYDESGPSIVHHK X 0.8046 0.026030.1087 0.8907 1.96E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 103P32582 72 56396 0 CBS_YEAST Cystathionine beta-synthase OS= Saccharomyces cerevisiae GN = CYS4 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 104 P01095 71 8585 0IPB2_YEAST Protease B inhibitors 2 and 1 OS = Saccharomyces cerevisiaeGN = PBI2 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 HNDVIENVEEDKEVHTN 0.7575 0.017050.129 0.6437 5.58E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 105Q00955 71 250197 0.8507 1 ACAC_YEAST Acetyl-CoA carboxylase OS= Saccharomyces cerevisiae GN = FAS3 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2QLSDGGLLIAIGGK X 0.8507 0.01702 0.06509 0.973 1.45E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 106 P22203 70 26455 0 VATE_YEAST V-typeproton ATPase subunit E OS = Saccharomyces cerevisiae GN = VMA4 PE = 1SV = 4 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 EQSLDGIFEETK 0.3294 0.1126 0.06772 0.69133.41E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 107 P38249 70110276 0.9265 1 EIF3A_YEAST Eukaryotic translation initiation factor 3subunit A OS = Saccharomyces cerevisiae GN = TIF32 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 TAGGSSPATPATPATPA X 0.9265 0.00916 0.2441 0.99257.88E+04 TPTPSSGPK Hit Accession Score Mass L/(L + H) SD (geo) # 108P09435 69 70504 0 HSP73_YEAST Heat shock protein SSA3 OS = Saccharomycescerevisiae GN = SSA3 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 109 P32588 69 50758 0 PUB1_YEAST Nuclear andcytoplasmic polyadenylated RNA-binding protein PUB1 OS = Saccharomycescerevisiae GN = PUB1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 QYFQVGGPIANIK 0.99470.002 0.3581 0.3382 2.32E+05 Hit Accession Score Mass L/(L + H) SD (geo)# 110 P53900 68 15171 0.05129 1 PFD4_YEAST Prefoldin subunit 4 OS= Saccharomyces cerevisiae GN = GIM3 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2NNTQVTFEDQQK X 0.05129 0.3627 0.09004 0.7859 1.49E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 111 P40825 68 107940 0 SYAC_YEASTAlanyl-tRNA synthetase, cytoplasmic OS = Saccharomyces cerevisiae GN= ALA1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 TFFETNENAPYLVK 0.9828 0.005320.346 0.5419 8.94E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 112P38631 68 214712 0 FKS1_YEAST 1,3-beta-glucan synthase component FKS1 OS= Saccharomyces cerevisiae GN = FKS1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3ILAEETAAYEGNENEAE 0.01026 1.465 0.2542 0.6992 1.23E+05 KEDALK HitAccession Score Mass L/(L + H) SD (geo) # 113 P47079 67 61952 0TCPQ_YEAST T-complex protein 1 subunit theta OS = Saccharomycescerevisiae GN = CCT8 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 114 P38205 66 78319 0 NCL1_YEAST tRNA(cytosine-5-)-methyltransferase NCL1 OS = Saccharomyces cerevisiae GN= NCL1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LSSETPALESEGPQTK 0.5913 0.049670.1079 0.3943 3.39E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 115P39939 65 13438 0 RS26B_YEAST 40S ribosomal protein S26-B OS= Saccharomyces cerevisiae GN = RPS26B PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2DLSEASVYPEYALPK 0.3176 0.05414 0.1397 0.3309 6.58E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 116 P35189 64 27423 0.8078 1 TAF14_YEASTTranscription initiation factor TFIID subunit 14 OS = Saccharomycescerevisiae GN = TAF14 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SGSTEETTANTGTIGK X0.8078 0.02101 0.0963 0.9487 1.58E+04 Hit Accession Score Mass L/(L + H)SD (geo) # 117 Q08972 64 134247 0 NEW1_YEAST [NU+] prion formationprotein 1 OS = Saccharomyces cerevisiae GN = NEW1 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 ASNLAKPSVDDDDSPAN 0.3162 0.05206 0.143 0.3829 2.23E+05IK Hit Accession Score Mass L/(L + H) SD (geo) # 118 P05736 63 273920.622 1.054 2 RL2_YEAST 60S ribosomal protein L2 OS = Saccharomycescerevisiae GN = RPL2A PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 KVISSDAR X 0.57770.00446 0.06036 0.9809 2.68E+04 2 3 ASLNVGNVLPLGSVPEG X 0.624 0.007640.308 0.9797 6.09E+05 TIVSNVEEKPGDR Hit Accession Score Mass L/(L + H)SD (geo) # 119 P06367 61 14600 0 RS14A_YEAST 40S ribosomal protein S14-AOS = Saccharomyces cerevisiae GN = RPS14A PE = 1 SV = 5 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 120 Q03195 60 68297 0.3246 1RLI1_YEAST Translation initiation factor RLI1 OS = Saccharomycescerevisiae GN = RLI1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 FDDPPEWQEIIK X 0.32460.05303 0.04664 0.8258 2.37E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 121 P23638 60 28697 0 PSA4_YEAST Proteasome component Y13 OS= Saccharomyces cerevisiae GN = PRE9 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 122 P33327 60 124254 0.99111.026 2 DHE2_YEAST NAD-specific glutamate dehydrogenase OS= Saccharomyces cerevisiae GN = GDH2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2GDIESISDK X 1.001 0.00158 0.3693 0.9924 5.15E+05 2 2 LVSFWAPESELK X0.957 0.01189 0.05111 0.9876 1.49E+05 3 3 RNDTTLLEIVENLK 0.1906 0.24540.2091 0.5903 2.89E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 123P17076 59 28107 0.7946 1 RL8A_YEAST 60S ribosomal protein L8-A OS= Saccharomyces cerevisiae GN = RPL8A PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2YRPETAAEK X  0.7946 0.00569 0.2624 0.987 1.02E+05 2 3 SKQDASPKPYAVK−0.000859 3.397 0.2839 0.2521 2.27E+05 Hit Accession Score Mass L/(L+ H) SD (geo) # 124 P00815 58 87666 0 HIS2_YEAST Histidine biosynthesistrifunctional protein OS = Saccharomyces cerevisiae GN = HIS4 PE = 1 SV= 3 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 IKEEAEELTEAK 0.1694 0.3439 0.09508 0.2327 1.01E+05 HitAccession Score Mass L/(L + H) SD (geo) # 125 P02309 57 11361 0 H4_YEASTHistone H4 OS = Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 DSVTYTEHAK 0.3491 0.08223 0.2286 0.1483 5.70E+05 HitAccession Score Mass L/(L + H) SD (geo) # 126 P37299 57 8587 0.04592 1QCR10_YEAST Cytochrome b-c1 complex subunit 10 OS = Saccharomycescerevisiae GN = QCR10 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 IPLLGPTLEDHTPPEDKPN X0.04592 0.3578 0.08934 0.7487 1.68E+05 Hit Accession Score Mass L/(L+ H) SD (geo) # 127 P23287 55 63355 1 1 PP2B1_YEASTSerine/threonine-protein phosphatase 2B catalytic subunit A1 OS= Saccharomyces cerevisiae GN = CNA1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3ILNMSTVALSKEPNLLKLK X 1 0.001 0.05272 0.9692 2.68E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 128 P38011 54 34784 0.7242 1 GBLP_YEASTGuanine nucleotide-binding protein subunit beta-like protein OS= Saccharomyces cerevisiae GN = ASC1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3VFSLDPQYLVDDLRPEF X 0.7242 0.00801 0.4127 0.9795 8.90E+05 AGYSK HitAccession Score Mass L/(L + H) SD (geo) # 129 P53200 54 28564 0.5579 1AML1_YEAST N(6)-adenine-specific DNA methyltransferase-like 1 OS= Saccharomyces cerevisiae GN = AML1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2EEQQHQEAFQK X 0.5579 0.1156 0.04329 0.7172 6.21E+04 Hit Accession ScoreMass L/(L + H) SD (geo) # 130 P32190 52 80158 0 GLPK_YEAST Glycerolkinase OS = Saccharomyces cerevisiae GN = GUT1 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity ModificationsHit Accession Score Mass L/(L + H) SD (geo) # 131 P19358 51 42470 0.99991 METK2_YEAST S-adenosylmethionine synthase 2 OS = Saccharomycescerevisiae GN = SAM2 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 TQLQKDIVEK X 0.99990.00317 0.04256 0.7785 2.46E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 132 Q12363 50 48353 0.7508 1 WTM1_YEAST Transcriptionalmodulator WTM1 OS = Saccharomyces cerevisiae GN = WTM1 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 YNPDDTIAPPQDATEES X 0.7508 0.002 0.7573 0.99782.44E+05 QTK Hit Accession Score Mass L/(L + H) SD (geo) # 133 P31539 47102533 0.8569 1 HS104_YEAST Heat shock protein 104 OS = Saccharomycescerevisiae GN = HSP104 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2 GADTNTPLEYLSK X0.8569 0.01624 0.2723 0.9822 3.21E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 134 P39935 46 107036 0.815 1 IF4F1_YEAST Eukaryoticinitiation factor 4F subunit p150 OS = Saccharomyces cerevisiae GN= TIF4631 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 LKETSDSTSTSTPTPTP X 0.8150.05328 0.1577 0.8433 8.82E+04 STNDSK Hit Accession Score Mass L/(L + H)SD (geo) # 135 P35732 46 83923 0.9125 1 YKF4_YEAST Uncharacterizedprotein YKL054C OS = Saccharomyces cerevisiae GN = YKL054C PE = 1 SV = 1z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 3 EQVKEEEQTAEELEQE X 0.9125 0.02943 0.623 0.98471.75E+05 QDNVAAPEEEVTVVEEK Hit Accession Score Mass L/(L + H) SD (geo) #136 P17255 45 119131 0 VATA_YEAST V-type proton ATPase catalytic subunitA OS = Saccharomyces cerevisiae GN = TFP1 PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 137 P02294 45 14229 0.8421 1H2B2_YEAST Histone H2B.2 OS = Saccharomyces cerevisiae GN = HTB2 PE = 1SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 QTHPDTGISQK X 0.8421 0.00914 0.1463 0.92181.30E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 138 P02293 4514244 0.8421 1 H2B1_YEAST Histone H2B.1 OS = Saccharomyces cerevisiae GN= HTB1 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 QTHPDTGISQK X 0.8421 0.009140.1463 0.9218 1.30E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 139P05749 43 13789 0 RL22A_YEAST 60S ribosomal protein L22-A OS= Saccharomyces cerevisiae GN = RPL22A PE = 1 SV = 3 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 140 P40204 43 8477 1 1RUXG_YEAST Small nuclear ribonucleoprotein G OS = Saccharomycescerevisiae GN = SMX2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 KVAGILR X 1 0 0.076890.9937 4.35E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 141 P0851843 139256 0 RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 OS= Saccharomyces cerevisiae GN = RPB2 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 142 P05755 43 22421 0RS9B_YEAST 40S ribosomal protein S9-B OS = Saccharomyces cerevisiae GN= RPS9B PE = 1 SV = 4 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 143 Q01855 43 15992 0 RS15_YEAST 40S ribosomal protein S15 OS= Saccharomyces cerevisiae GN = RPS15 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2LLEMSTEDFVK 0.384 0.05738 0.2239 0.6167 5.45E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 144 P26781 42 17898 1 1 RS11_YEAST 40Sribosomal protein S11 OS = Saccharomyces cerevisiae GN = RPS11A PE = 1SV = 3 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 1 NAGLGFK X 1 0 0.701 0.9998 2.17E+06 HitAccession Score Mass L/(L + H) SD (geo) # 145 P00950 42 27784 0PMG1_YEAST Phosphoglycerate mutase 1 OS = Saccharomyces cerevisiae GN= GPM1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 146 P32380 41 112692 0.9554 1 NUF1_YEAST Protein NUF1 OS= Saccharomyces cerevisiae GN = NUF1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 IIDLQKK0.9984 0.00413 0.00899 0.6498 1.06E+04 2 2 IEIENWK X 0.9554 0.010280.1168 0.9842 1.57E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 147P16120 41 57439 0 THRC_YEAST Threonine synthase OS = Saccharomycescerevisiae GN = THR4 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 3 LYIAQEEIPDADLKDLIK0.04854 0.3108 0.1234 0.3822 1.17E+06 Hit Accession Score Mass L/(L + H)SD (geo) # 148 P43616 41 52838 0.6185 1 DUG1_YEAST Cys-Glymetallodipeptidase DUG1 OS = Saccharomyces cerevisiae GN = DUG1 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 ILIDGIDEMVAPLTEK X 0.6185 0.00821 0.11150.9559 3.58E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 149 P2529438 37567 0.5309 1 SIS1_YEAST Protein SIS1 OS = Saccharomyces cerevisiaeGN = SIS1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 YHPDKPTGDTEK X 0.5309 0.056980.03541 0.7338 2.13E+05 Hit Accession Score Mass L/(L + H) SD (geo) #150 P0C0T4 37 12002 0.8113 1 RS25B_YEAST 40S ribosomal protein S25-B OS= Saccharomyces cerevisiae GN = RPS25B PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 3AQHAVILDQEK X 0.8113 0.04438 0.03423 0.7174 2.04E+04 2 3 AQHAVILDQEKYDR0.1884 0.06967 0.3797 0.1743 2.54E+06 Hit Accession Score Mass L/(L + H)SD (geo) # 151 Q08438 37 73997 0 VHS3_YEAST Protein VHS3 OS= Saccharomyces cerevisiae GN = VHS3 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 152 Q05506 36 69890 0SYRC_YEAST Arginyl-tRNA synthetase, cytoplasmic OS = Saccharomycescerevisiae GN = YDR341C PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 2 YGNEEALVK 0.18290.1367 0.1933 0.1382 3.93E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 153 P06168 36 44565 0 ILV5_YEAST Ketol-acid reductoisomerase,mitochondrial OS = Saccharomyces cerevisiae GN = ILV5 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 154 P3816736 123534  0.5931 1 ECM21_YEAST Protein ECM21 OS = Saccharomycescerevisiae GN = ECM21 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SRFNNLDK X 0.59310.03207 0.03169 0.8355 1.66E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 155 P04076 34 52173 0 ARLY_YEAST Argininosuccinate lyase OS= Saccharomyces cerevisiae GN = ARG4 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 156 P61864 33  8552 0.8436 1UBIQ_YEAST Ubiquitin OS = Saccharomyces cerevisiae GN = UBI1 PE = 1 SV= 1 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 IQDKEGIPPDQQR X 0.8436 0.00578 0.2069 0.9679 1.11E+06Hit Accession Score Mass L/(L + H) SD (geo) # 157 P54839 33 55324 0HMCS_YEAST Hydroxymethylglutaryl-CoA synthase OS = Saccharomycescerevisiae GN = ERG13 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 158 P40482 33 103842  0 SEC24_YEAST Proteintransport protein SEC24 OS = Saccharomyces cerevisiae GN = SEC24 PE = 1SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) #159 P05694 31 85807 0 METE_YEAST5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase OS= Saccharomyces cerevisiae GN = MET6 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3APEQFDEVVAAIGNK 0.8993 0.03287 0.3114 0.6099 7.32E+05 Hit AccessionScore Mass L/(L + H) SD (geo) # 160 P0C0W1 31 14705 0 RS22A_YEAST 40Sribosomal protein S22-A OS = Saccharomyces cerevisiae GN = RPS22A PE = 1SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications Hit Accession Score Mass L/(L + H) SD (geo) #161 P06105 30 135689  0 SC160_YEAST Protein SCP160 OS = Saccharomycescerevisiae GN = SCP160 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std.Err. Fraction Correlation Intensity Modifications 1 3 FQFLIDAEELKEK0.2574 0.1495 0.03011 0.4086 8.22E+04 Hit Accession Score Mass L/(L + H)SD (geo) # 162 P14065 30 35057 0.8654 1 GCY_YEAST Protein GCY OS= Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 GYVVLPKX 0.8654 0.0811 0.06444 0.8822 3.00E+04 Hit Accession Score Mass L/(L+ H) SD (geo) # 163 P52490 29 17561 0 UBC13_YEAST Ubiquitin-conjugatingenzyme E2 13 OS = Saccharomyces cerevisiae GN = UBC13 PE = 1 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 164 P3899428 89754 0 MSS4_YEAST Probable phosphatidylinositol-4-phosphate 5-kinaseMSS4 OS = Saccharomyces cerevisiae GN = MSS4 PE = 1 SV = 2 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 ISAVTATSTTIK −0.000063 7.067 0.305 0.9995 4.66E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 165 P32893 28 63328 0 KRE11_YEAST Beta-glucansynthesis-associated protein KRE11 OS = Saccharomyces cerevisiae GN= KRE11 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 ASEQLTKK 0.3303 0.2361 0.020430.1669 9586 Hit Accession Score Mass L/(L + H) SD (geo) # 166 A6ZPZ1 2895169 0.999 1 YJ00_YEAS7 UPF0508 protein SCY_2952 OS = Saccharomycescerevisiae (strain YJM789) GN = SCY_2952 PE = 3 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2SIQVPLSPK X 0.999 0.00323 0.07993 0.9881 3.06E+05 Hit Accession ScoreMass L/(L + H) SD (geo) # 167 P15891 28 65536 0 ABP1_YEAST Actin-bindingprotein OS = Saccharomyces cerevisiae GN = ABP1 PE = 1 SV = 4 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 AEAPKPEVPEDEPEGEP 0.2106 0.08472 0.3799 0.4288 9.13E+05 DVK HitAccession Score Mass L/(L + H) SD (geo) # 168 P32074 27 105239  0.8225 1COPG_YEAST Coatomer subunit gamma OS = Saccharomyces cerevisiae GN= SEC21 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 SETTLDTTPEAESVPEKR X 0.82250.02368 0.1323 0.7806 1.44E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 169 P04801 27 84987 0 SYTC_YEAST Threonyl-tRNA synthetase,cytoplasmic OS = Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 170 B3RHV027 28726 0.954 1 RS3A1_YEAS1 40S ribosomal protein S1-A OS= Saccharomyces cerevisiae (strain RM11-1a) GN = RPS1A PE = 3 SV = 1 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications 1 2 LRVDEVQGK X 0.954 0.00845 0.1571 0.9013 1.03E+06 HitAccession Score Mass L/(L + H) SD (geo) # 171 Q01217 27 95307 0ARG56_YEAST Protein ARG5,6, mitochondrial OS = Saccharomyces cerevisiaeGN = ARG5,6 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications Hit Accession Score Mass L/(L + H)SD (geo) # 172 P32861 27 56234 0.7068 1 UGPA1_YEASTUTP--glucose-1-phosphate uridylyltransferase OS = Saccharomycescerevisiae GN = UGP1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 YEIISQQPENVSNLSK X0.7068 0.00158 0.1676 0.9848 2.66E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 173 Q12462 27 26995 0 PEX11_YEAST Peroxisomal membraneprotein PMP27 OS = Saccharomyces cerevisiae GN = PEX11 PE = 1 SV = 2 zSequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 174 P5358327 61628 0.9997 1 MPA43_YEAST Protein MPA43 OS = Saccharomycescerevisiae GN = MPA43 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 ALQKCLQKLNIR X 0.9997 00.5408 0.9792 4.03E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 175P38737 26 211316  1 1 ECM29_YEAST Proteasome component ECM29 OS= Saccharomyces cerevisiae GN = ECM29 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2LKNLLR X 1 0 0.07689 0.9937 4.35E+05 Hit Accession Score Mass L/(L + H)SD (geo) # 176 P40494 26 90976 1 1 PRK1_YEAST Actin-regulating kinasePRK1 OS = Saccharomyces cerevisiae GN = PRK1 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 LKNLIR X 1 0 0.07689 0.9937 4.35E+05 Hit Accession Score Mass L/(L+ H) SD (geo) # 177 P36048 26 114578  1 1 SN114_YEAST 114 kDa U5 smallnuclear ribonucleoprotein component OS = Saccharomyces cerevisiae GN= SNU114 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LKNLLR X 1 0 0.07689 0.99374.35E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 178 Q01846 26130637  0.08842 1 MDM1_YEAST Structural protein MDM1 OS = Saccharomycescerevisiae GN = MDM1 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 TKIYIR X 0.08842 0.10270.1197 0.9815 7.92E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 179P04456 26 15924 0 RL25_YEAST 60S ribosomal protein L25 OS= Saccharomyces cerevisiae GN = RPL25 PE = 1 SV = 4 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 180 Q99186 24 55352 1.007 1AP2M_YEAST AP-2 complex subunit mu OS = Saccharomyces cerevisiae GN= APM4 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 HSGSDFGNK X 1.007 0.007750.03715 0.9671 4599 Hit Accession Score Mass L/(L + H) SD (geo) # 181Q04922 23 53135 0.9994 1 MFB1_YEAST Mitochondrial F-box protein MFB1 OS= Saccharomyces cerevisiae GN = MFB1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 KDNPRLKX 0.9994 0.00158 0.4699 0.9983 3.45E+06 Hit Accession Score Mass L/(L+ H) SD (geo) # 182 Q03786 23 22353 0 GNTK_YEAST Probable gluconokinaseOS = Saccharomyces cerevisiae GN = YDR248C PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 12 KYRDLIR 0.000004 1211 0.06617 0.9937 3.09E+04 Hit Accession Score MassL/(L + H) SD (geo) # 183 P04147 23 64304 0 PABP_YEASTPolyadenylate-binding protein, cytoplasmic and nuclear OS= Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2YQGVNLFVK 0.6493 0.04431 0.1257 0.2785 2.62E+05 Hit Accession Score MassL/(L + H) SD (geo) # 184 P13663 23 39519 0 DHAS_YEASTAspartate-semialdehyde dehydrogenase OS = Saccharomyces cerevisiae GN= HOM2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 IREDPLLDFK 0.18 0.182 0.081090.1847 7.16E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 185 P1909723 207964  0 FAS2_YEAST Fatty acid synthase subunit alpha OS= Saccharomyces cerevisiae GN = FAS2 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications HitAccession Score Mass L/(L + H) SD (geo) # 186 P38264 23 21123 0PHO88_YEAST Inorganic phosphate transport protein PHO88 OS= Saccharomyces cerevisiae GN = PHO88 PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2SALEHNEVK 0.942 0.01455 0.09329 0.575 5.32E+04 Hit Accession Score MassL/(L + H) SD (geo) # 187 P33203 23 69023 0.9927 1 PRP40_YEASTPre-mRNA-processing protein PRP40 OS = Saccharomyces cerevisiae GN= PRP40 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 YLSNRSADQLLK X 0.9927 0.004120.2098 0.996 4.72E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 188P32386 22 189043  0 YBT1_YEAST ATP-dependent bile acid permease OS= Saccharomyces cerevisiae GN = YBT1 PE = 1 SV = 2 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 IFNMILNK0.004101 0.9579 0.2443 0.5181 1.15E+06 Hit Accession Score Mass L/(L+ H) SD (geo) # 189 P40075 22 26909 0 SCS2_YEAST Vesicle-associatedmembrane protein-associated protein SCS2 OS = Saccharomyces cerevisiaeGN = SCS2 PE = 1 SV = 3 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 3 YLISPDVHPAQNQNIQE 0.6453 0.10210.2303 0.4558 6.49E+04 NK Hit Accession Score Mass L/(L + H) SD (geo) #190 Q06685 22 129674  1.008 1 VIP1_YEAST Inositol hexakisphosphate anddiphosphoinositol-pentakisphosphate kinase OS = Saccharomyces cerevisiaeGN = VIP1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 SSTSHPKPR X 1.008 0.021170.06128 0.7799 7778 Hit Accession Score Mass L/(L + H) SD (geo) # 191P46962 21 38057 0 CTK2_YEAST CTD kinase subunit beta OS = Saccharomycescerevisiae GN = CTK2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications Hit Accession Score MassL/(L + H) SD (geo) # 192 P13188 21 93075 0.9115 1 SYQ_YEASTGlutaminyl-tRNA synthetase OS = Saccharomyces cerevisiae GN = GLN4 PE= 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 SDFSENVDDKEFFR X 0.9115 0.00801 0.18430.8822 6.60E+05 Hit Accession Score Mass L/(L + H) SD (geo) # 193 Q0220821 86313 0.9576 1 TOF2_YEAST Topoisomerase 1-associated factor 2 OS= Saccharomyces cerevisiae GN = TOF2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2AESKDLDLLR X 0.9576 0.00992 0.5313 0.8332 4.35E+06 Hit Accession ScoreMass L/(L + H) SD (geo) # 194 P43544 21 25116 0.9621 1 SNO3_YEASTProbable glutamine amidotransferase SNO3 OS = Saccharomyces cerevisiaeGN = SNO3 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 LDGKDNGGQELIVAAK X 0.96210.00918 0.1046 0.9559 1.74E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 195 P53254 21 141262  0 UTP22_YEAST U3 small nucleolarRNA-associated protein 22 OS = Saccharomyces cerevisiae GN = UTP22 PE= 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. Fraction CorrelationIntensity Modifications 1 2 LSERLTLAQYK 0.002931 1.18 0.313 0.99681.09E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 196 Q12507 2138997 0.9995 1 SFG1_YEAST Superficial pseudohyphal growth protein 1 OS= Saccharomyces cerevisiae GN = SFG1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 TSSKNVKX 0.9995 0.00158 0.4979 0.9993 2.25E+06 Hit Accession Score Mass L/(L+ H) SD (geo) # 197 Q06625 20 175551  0 GDE_YEAST Glycogen debranchingenzyme OS = Saccharomyces cerevisiae GN = GDB1 PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity ModificationsHit Accession Score Mass L/(L + H) SD (geo) # 198 P17555 20 57486 0.71161 CAP_YEAST Adenylyl cyclase-associated protein OS = Saccharomycescerevisiae GN = SRV2 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 SDGGNIYLSK X 0.71160.00648 0.07351 0.9734 7.93E+04 Hit Accession Score Mass L/(L + H) SD(geo) # 199 Q12345 20 28402 0 IES3_YEAST Ino eighty subunit 3 OS= Saccharomyces cerevisiae GN = IES3 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 3IDILTKIQENLLEEYQK 0.7775 0.1023 0.03577 0.4115 952.5 Hit Accession ScoreMass L/(L + H) SD (geo) # 200 P32802 20 75914 0.9962 1 TMN1_YEASTTransmembrane 9 superfamily member 1 OS = Saccharomyces cerevisiae GN= EMP70 PE = 1 SV = 2 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 KIYSSIK X 0.9962 0.02516 0.039190.9666 1.24E+04 Hit Accession Score Mass L/(L + H) SD (geo) # 201 P5329520 40980 0.9333 1 YG3Y_YEAST Uncharacterized GTP-binding protein YGR173WOS = Saccharomyces cerevisiae GN = YGR173W PE = 1 SV = 1 z SequenceIncl. L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 13 CLYVYNKIDAVSLEEVDK X 0.9333 0.01137 0.1522 0.9687 5.58E+05 HitAccession Score Mass L/(L + H) SD (geo) # 202 P53244 20 65724 0.03843 1ART5_YEAST Arrestin-related trafficking adapter 5 OS = Saccharomycescerevisiae GN = ART5 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err.Fraction Correlation Intensity Modifications 1 2 GRLVLFDK X 0.038430.07779 0.03009 0.8963 8.52E+05 Hit Accession Score Mass L/(L + H) SD(geo) # 203 P53598 20 35010 0.9917 1 SUCA_YEAST Succinyl-CoA ligase[ADP-forming] subunit alpha, mitochondrial OS = Saccharomyces cerevisiaeGN = LSC1 PE = 1 SV = 1 z Sequence Incl. L/(L + H) Std. Err. FractionCorrelation Intensity Modifications 1 2 ESIPYDK X 0.9917 0.001 0.44950.9852 2.95E+06 Hit Accession Score Mass L/(L + H) SD (geo) # 204 P4852419    109107.00 0 BUL1_YEAST Ubiquitin ligase-binding protein BUL1 OS= Saccharomyces cerevisiae GN = BUL1 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 SPSLHSPK0.5209 0.06221 0.06108 0.3577 1.00E+05 Hit Accession Score Mass L/(L+ H) SD (geo) # 205 P35172 19 89623 0 TREB_YEAST Probable trehalase OS= Saccharomyces cerevisiae GN = NTH2 PE = 1 SV = 1 z Sequence Incl. L/(L+ H) Std. Err. Fraction Correlation Intensity Modifications 1 2 RAFRAAIK0.05024 0.1466 0.00365 0.2201 1.25E+04 Hit Accession Score Mass L/(L+ H) SD (geo) # 206 P10963 18 61201 0 PCKA_YEAST Phosphoenolpyruvatecarboxykinase [ATP] OS = Saccharomyces cerevisiae GN = PCK1 PE = 1 SV= 2 z Sequence Incl. L/(L + H) Std. Err. Fraction Correlation IntensityModifications Hit Accession Score Mass L/(L + H) SD (geo) # 207 P5313318 30896 0.8643 1 YGL7_YEAST Uncharacterized protein YGL117W OS= Saccharomyces cerevisiae GN = YGL117W PE = 1 SV = 1 z Sequence Incl.L/(L + H) Std. Err. Fraction Correlation Intensity Modifications 1 2TSLKITHRR X 0.8643 0.01604 0.0279 0.7852 9.11E+04 Hit Accession ScoreMass L/(L + H) SD (geo) # 208 Q07913 17 38310 0 NSE1_YEASTNon-structural maintenance of chromosomes element 1 OS = Saccharomycescerevisiae GN = NSE1 PE = 1 SV = 1

TABLE 3 Ribosomal proteins used to establish the non-specificallyassociating baseline for ChAP-MS analyses. The percentage light andstandard deviation are listed for each ribosomal protein. Stdev StdevRibosomal Proteins Glucose Glucose Galactose Galactose 40S ribosomalprotein S10-A OS = Saccharomyces cerevisiae GN = RPS10A 48.01% 1.14%65.47% 0.00% PE = 1 SV = 1 40S ribosomal protein S17-A OS =Saccharomyces cerevisiae GN = RPS17A 47.77% 0.00% 70.60% 4.47% PE = 1 SV= 1 40S ribosomal protein S21-A OS = Saccharomyces cerevisiae GN =RPS21A 53.30% 1.79% 56.17% 1.13% PE = 1 SV = 1 60S ribosomal proteinL14-B OS = Saccharomyces cerevisiae GN = RPL14B 52.21% 4.40% 77.37%10.01% PE = 1 SV = 1 60S ribosomal protein L19 OS = Saccharomycescerevisiae GN = RPL19A PE = 1 50.26% 1.25% 71.05% 5.03% SV = 5 60Sribosomal protein L26-A OS = Saccharomyces cerevisiae GN = RPL26A 51.09%0.00% 70.20% 0.00% PE = 1 SV = 3 60S ribosomal protein L3 OS =Saccharomyces cerevisiae GN = RPL3 PE = 1 49.39% 5.09% 66.83% 7.02% SV =4 60S ribosomal protein L30 OS = Saccharomyces cerevisiae GN = RPL30 PE= 1 48.85% 4.03% 62.85% 4.95% SV = 3 40S ribosomal protein S12 OS =Saccharomyces cerevisiae GN = RPS12 PE = 1 50.92% 13.06% 78.21% 1.50% SV= 1 40S ribosomal protein S19-A OS = Saccharomyces cerevisiae GN =RPS19A 49.03% 1.43% 59.47% 1.64% PE = 1 SV = 2 40S ribosomal proteinS26-A OS = Saccharomyces cerevisiae GN = RPS26A 50.63% 2.36% 71.70%4.02% PE = 1 SV = 1 40S ribosomal protein S4 OS = Saccharomycescerevisiae GN = RPS4A PE = 1 44.54% 11.51% 54.31% 4.61% SV = 3 40Sribosomal protein S7-A OS = Saccharomyces cerevisiae GN = RPS7A 51.87%2.38% 75.86% 6.19% PE = 1 SV = 4 40S ribosomal protein S11 OS =Saccharomyces cerevisiae GN = RPS11A 49.48% 3.94% 74.42% 3.71% PE = 1 SV= 3 60S acidic ribosomal protein P0 OS = Saccharomyces cerevisiae GN =RPP0 50.01% 2.91% 62.25% 3.64% PE = 1 SV = 1 60S ribosomal protein L10OS = Saccharomyces cerevisiae GN = RPL10 PE = 1 53.45% 2.89% 63.81%2.66% SV = 1 60S ribosomal protein L12 OS = Saccharomyces cerevisiae GN= RPL12A PE = 1 51.79% 1.15% 66.76% 2.02% SV = 1 60S ribosomal proteinL30 OS = Saccharomyces cerevisiae GN = RPL30 PE = 1 48.85% 4.03% 63.49%4.82% SV = 3 60S ribosomal protein L9-A OS = Saccharomyces cerevisiae GN= RPL9A PE = 1 49.58% 3.07% 58.70% 2.73% SV = 2 40S ribosomal proteinS1-B OS = Saccharomyces cerevisiae (strain YJM789) 47.63% 4.27% 75.33%9.16% GN = RPS1B PE = 3 SV = 1

TABLE 4 Proteins and PTMs specifically associating with GAL1 chromatinisolated from cells cultured in galactose. Proteins and histoneposttranslational modifications listed are greater than two standarddeviations from the non-specific threshold (80.9% Light). % Light StdevProtein Name Glucose Glucose DNA-directed RNA polymerase II 140 kDapolypeptide (EC 2.7.7.6) (B150)- S cerevisiae 100.00% 0.00% HistoneH3K18acK23ac 100.00% 0.00% Histone H2A.1 OS = Saccharomyces cerevisiaeGN = HTA1 PE = 1 SV = 2 97.10% 6.02% NAD-specific glutamatedehydrogenase OS = Saccharomyces cerevisiae GN = GDH2 PE = 1 SV = 196.09% 2.70% Histone H4K5acK8ac 95.89% 0.00% DNA-directed RNA polymeraseII largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1) (B220) -94.36% 4.99% S cerevisiae Histone H3K9acK14ac 93.62% 0.00% HistoneH4K12acK16ac 90.56% 3.00% Histone H2B.1 OS = Saccharomyces cerevisiae GN= HTB1 PE = 1 SV = 2 89.59% 9.51% Acetyl-CoA carboxylase OS =Saccharomyces cerevisiae GN = FAS3 PE = 1 SV = 2 89.04% 3.39%6-phosphogluconate dehydrogenase, decarboxylating 1 OS = Saccharomycescerevisiae GN = GND1 PE = 1 87.74% 3.05% SV = 1 Probableinosine-5′-monophosphate dehydrogenase IMD3 OS = Saccharomycescerevisiae GN = IMD3 87.19% 14.00% PE = 1 SV = 1 Eukaryotic translationinitiation factor 3 subunit A OS = Saccharomyces cerevisiae GN = TIF32PE = 1 SV = 1 86.97% 7.61% Histone H3K14ac 85.83% 4.48% Histone H3 OS =Saccharomyces cerevisiae GN = HHT1 PE = 1 SV = 2 85.83% 4.48% Zuotin OS= Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1 85.33% 5.43% ProteinGCY OS = Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1 85.18% 7.02%Histone H4 OS = Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2 90.42%8.84% Actin-related protein 2/3 complex subunit 4 OS = Saccharomycescerevisiae GN = ARC19 PE = 1 SV = 2 84.74% 4.60%Translationally-controlled tumor protein homolog OS = Saccharomycescerevisiae GN = TMA19 PE = 1 SV = 1 84.64% 1.50% Suppressor protein STM1OS = Saccharomyces cerevisiae GN = STM1 PE = 1 SV = 3 84.58% 5.36% FACTcomplex subunit SPT16 OS = Saccharomyces cerevisiae GN = SPT16 PE = 1 SV= 1 84.24% 3.60% Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE= 1 SV = 4 84.22% 5.92% Alcohol dehydrogenase 1 OS = Saccharomycescerevisiae GN = ADH1 PE = 1 SV = 4 83.55% 11.23% Pyruvate carboxylase 1OS = Saccharomyces cerevisiae GN = PYC1 PE = 1 SV = 2 82.51% 7.74%Protein GAL3 OS = Saccharomyces cerevisiae GN = GAL3 PE = 1 SV = 281.95% 8.37% Cell division control protein 48 OS = Saccharomycescerevisiae GN = CDC48 PE = 1 SV = 3 80.99% 2.13%

TABLE 5 Proteins and PTMs specifically associating with GAL1 chromatinisolated from cells cultured in glucose. Proteins and histoneposttranslational modifications listed are greater than two standarddeviations from the non-specific threshold (56.18% Light). % Light StdevProtein Name Glucose Glucose Histone H3K36me3 100.00% 0.00%Glucose-6-phosphate isomerase OS = Saccharomyces cerevisiae GN = PGI1 PE= 1 SV = 3 66.33% 12.98% Magnesium-activated aldehyde dehydrogenase,cytosolic OS = Saccharomyces cerevisiae GN = ALD6 58.78% 9.50% PE = 1 SV= 4 Phosphoglycerate mutase 1 OS = Saccharomyces cerevisiae GN = GPM1 PE= 1 SV = 3 58.62% 6.39% Plasma membrane ATPase 1 OS = Saccharomycescerevisiae GN = PMA1 PE = 1 SV = 2 58.47% 6.81% Cystathioninegamma-lyase OS = Saccharomyces cerevisiae GN = CYS3 PE = 1 SV = 2 58.10%3.72% Enolase 1 OS = Saccharomyces cerevisiae GN = ENO1 PE = 1 SV = 257.88% 2.93% Enolase 2 OS = Saccharomyces cerevisiae GN = ENO2 PE = 1 SV= 2 57.40% 2.33% Heat shock protein SSA4 OS = Saccharomyces cerevisiaeGN = SSA4 PE = 1 SV = 3 56.99% 4.82% Cell division control protein 48 OS= Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3 56.59% 4.13%Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE = 1 SV = 456.50% 3.43% Fatty acid synthase subunit alpha OS = Saccharomycescerevisiae GN = FAS2 PE = 1 SV = 2 56.19% 6.29%

TABLE 6TAL protein DNA-binding specificity. ChIP was performed for the TAL-PrAused in this study and relative genomic binding was measured with qPCR at eachsequence listed below.Real time qPCR primers were used to amplify regions containing the indicated sequences andenrichment of each was measured relative to ACT1. The standard error of three analyses is shown. The first listed DNA sequence at GAL1 (highlighed gray) was used to design the TAL protein. A BLAST search was used to identify the next five closest binding sites in the S. cerevisiae  genome. Mismatches of these five sequences relative to the GAL1 sequence are shown in bold.ChIP-qPCR for Closest TAL-PrA binding Sequence Chromosome CoordinatesGene Locus tag Relative to Actin

ChrII 278829-278846 GAL1 YBR020W, promoter region 6.14 ± 0.28GGGGTAATTAATCATTTT ChrIV 823079-823066 SCC2 YDR180W 0.65 ± 0.06TTATACATTAATCAGCGA ChrXV 18844-18855 ENB1 between YOL159C and 1.34 ±0.13 YOL158C GGGGTAATTAATGTAAAT ChrXIV 614716-614705 IDP3YNL009W , promoter region 0.94 ± 0.46 AAATTAATCAGCGGTGAC ChrIX88064-88053 REV7 YIL139C 0.77 ± 0.27 GGGGTAATTAAAATTTCT ChrXVI94211-94221 IQG1 YPL242C 0.76 ± 0.10

TABLE 7 Significant proteins (>2-fold enriched) identified with GAL1promoter chromatin from cells grown in galactose-containing media. Thetop 10% of proteins that are >15- fold enriched are highlighted in gray.Spectral Spectral Counts Molecular Counts Wild Proteins Weight TAL-PrAtype

PMA1_YEAST 99,621.60 558 0

YH11 B_YEAST (+2) 202,825.20 273 0

DED1_YEAS7 (+1) 65,554.50 261 0

TIF31_YEAST 145,171.10 226 0

PYR1_YEAST 245,129.90 1356 3

EF3B_YEAST 115,871.60 220 0

YO11A_YEAST 49,006.10 216 0

RS3A2_YEAS1 (+3) 28,812.90 204 0

RS3A1_YEAS1 (+4) 28,743.80 189 0

YD12A_YEAST 49,187.40 188 0

GAL2_YEAST 63,627.00 183 0

ASSY_YEAST 46,941.00 177 0

PDR5_YEAST 170,444.10 152 0

FKS1_YEAST 214,859.40 151 0

HSP7E_YEAST 70,086.90 150 0

PDC6_YEAST 61,582.40 150 0

BFR1_YEAST 54,641.70 137 0

RL18_YEAST 20,563.70 129 0

RS2_YEAST 27,450.20 126 0

FKS2_YEAST 216,998.10 126 0

6PGD2_YEAST 53,925.30 118 0

HXT7_YEAST 62,736.00 108 0

GAL3_YEAST 58,130.40 107 0

MS116_YEAST 76,272.50 105 0

ATC6_YEAST 135,274.80 98 0

HXT6_YEAST 62,706.00 98 0

IF2P_YEAST 112,271.50 98 0

RPB1_YEAST 191,615.10 96 0

GAS1_YEAST 59,583.20 94 0

EIF3B_YEAS7 88,131.50 93 0

PGM1_YEAST 63,114.70 91 0

TCPG_YEAST 58,814.70 90 0

SPT16_YEAST 118,636.00 88 0

DBP1_YEAS7 (+1) 67,992.10 87 0

ODP2_YEAST 51,819.70 87 0

CLH_YEAST 187,243.20 173 1

RS8_YEAST 22,490.40 86 0

RPB2_YEAST 138,757.20 85 0

GLNA_YEAST 41,767.10 80 0

TOM40_YEAST 42,039.40 79 0

C1TC_YEAST 102,207.30 76 0

FBRL_YEAST 34,465.50 75 0

SC160_YEAST 134,813.70 300 2

SEC23_YEAST 85,387.60 73 0

NOP56_YEAST 56,867.30 73 0

PYRF_YEAST 29,240.40 71 0

HOSC_YEAST 47,100.30 68 0

NDH1_YEAST 62,776.50 67 0

EIF3C_YEAS7 93,225.20 67 0

ZUO1_YEAST 49,021.50 66 0

TPS2_YEAST 102,978.90 63 0

CARP_YEAST 44,501.00 63 0

RRP5_YEAST 193,141.40 63 0

KAPR_YEAST 47,220.30 62 0 Galactokinase OS = Saccharomyces cerevisiae GN= GAL1 PE = 1 SV = 4 GAL1_YEAST 57,945.00 1350 11 Probable2-methylcitrate dehydratase OS = Saccharomyces cerevisiae PRPD_YEAST57,685.70 61 0 GN = PDH1 PE = 1 SV = 1 2-isopropylmalate synthase 2,mitochondrial OS = Saccharomyces LEU9_YEAST 67,201.00 61 0 cerevisiae GN= LEU9 PE = 1 SV = 1 NADH-cytochrome b5 reductase 2 OS = Saccharomycescerevisiae MCR1_YEAST 34,109.10 61 0 (strain YJM789) GN = MCR1 PE = 2 SV= 1 (+1) 6,7-dimethyl-8-ribityllumazine synthase OS = SaccharomycesRIB4_YEAST 18,555.70 60 0 cerevisiae GN = RIB4 PE = 1 SV = 2N-(5′-phosphoribosyl)anthranilate isomerase OS = SaccharomycesTRPF_YEAST 24,144.90 60 0 cerevisiae GN = TRP1 PE = 1 SV = 2 Glutamatesynthase [NADH] OS = Saccharomyces cerevisiae GLT1_YEAST 238,108.30 58 0GN = GLT1 PE = 1 SV = 2 Nuclear localization sequence-binding protein OS= Saccharomyces NSR1_YEAST 44,536.10 55 0 cerevisiae GN = NSR1 PE = 1 SV= 1 V-type proton ATPase subunit a, vacuolar isoform VPH1_YEAST95,533.10 55 0 OS = Saccharomyces cerevisiae GN = VPH1 PE = 1 SV = 34-aminobutyrate aminotransferase OS = Saccharomyces cerevisiaeGATA_YEAST 52,948.60 55 0 GN = UGA1 PE = 1 SV = 2 Dihydroorotatedehydrogenase OS = Saccharomyces cerevisiae PYRD_YEAST 34,802.70 54 0 GN= URA1 PE = 1 SV = 1 Eukaryotic translation initiation factor 2A OS =Saccharomyces EIF2A_YEAST 71,307.10 54 0 cerevisiae GN = YGR054W PE = 1SV = 1 60S ribosomal protein L32 OS = Saccharomyces cerevisiae GN =RPL32 RL32_YEAST 14,771.80 53 0 PE = 1 SV = 1 60S ribosomal proteinL15-A OS = Saccharomyces cerevisiae RL15A_YEAST 24,422.60 105 1 GN =RPL15A PE = 1 SV = 3 Mitochondrial import receptor subunit TOM70 OS =Saccharomyces TOM70_YEAST 70,127.70 51 0 cerevisiae (strain YJM789) GN =TOM70 PE = 3 SV = 1 (+1) Mitochondrial acidic protein MAM33 OS =Saccharomyces cerevisiae MAM33_YEAST 30,132.70 51 0 GN = MAM33 PE = 1 SV= 1 H/ACA ribonucleoprotein complex subunit 4 OS = SaccharomycesCBF5_YEAST 54,706.30 51 0 cerevisiae GN = CBF5 PE = 1 SV = 1 60Sribosomal protein L8-A OS = Saccharomyces cerevisiae RL8A_YEAST28,125.50 201 2 GN = RPL8A PE = 1 SV = 4 Eukaryotic translationinitiation factor 2 subunit alpha IF2A_YEAST 34,718.70 50 0 OS =Saccharomyces cerevisiae GN = SUI2 PE = 1 SV = 1 NADPH--cytochrome P450reductase OS = Saccharomyces cerevisiae NCPR_YEAST 76,774.20 50 0 GN =NCP1 PE = 1 SV = 3 Nucleolar protein 58 OS = Saccharomyces cerevisiae(strain YJM789) NOP58_YEAS7 56,959.80 98 1 GN = NOP58 PE = 3 SV = 1 (+1)60S ribosomal protein L14-B OS = Saccharomyces cerevisiae RL14B_YEAST15,153.20 97 1 GN = RPL14B PE = 1 SV = 1 Pentafunctional AROMpolypeptide OS = Saccharomyces cerevisiae ARO1_YEAST 174,758.00 97 1 GN= ARO1 PE = 1 SV = 1 60S ribosomal protein L8-B OS = Saccharomycescerevisiae RL8B_YEAST 28,112.80 193 2 GN = RPL8B PE = 1 SV = 3GTP-binding protein RHO1 OS = Saccharomyces cerevisiae GN = RHO1RHO1_YEAST 23,152.00 48 0 PE = 1 SV = 3 Invertase 2 OS = Saccharomycescerevisiae GN = SUC2 PE = 1 SV = 1 INV2_YEAST 60,641.00 48 0 (+1)Squalene synthase OS = Saccharomyces cerevisiae GN = ERG9 PE = 1FDFT_YEAST 51,722.50 48 0 SV = 2 Eukaryotic translation initiationfactor 3 subunit B OS = Saccharomyces EIF3B_YEAST 88,131.50 95 1cerevisiae GN = PRT1 PE = 1 SV = 1 Cytochrome c iso-2 OS = Saccharomycescerevisiae GN = CYC7 PE = 1 CYC7_YEAST 12,532.80 47 0 SV = 1ATP-dependent permease PDR15 OS = Saccharomyces cerevisiae PDR15_YEAST172,261.80 47 0 GN = PDR15 PE = 1 SV = 1 60S ribosomal protein L28 OS =Saccharomyces cerevisiae GN = RPL28 RL28_YEAST 16,722.90 46 0 PE = 1 SV= 2 Methionyl-tRNA synthetase, cytoplasmic OS = Saccharomyces SYMC_YEAST85,680.90 46 0 cerevisiae GN = MES1 PE = 1 SV = 4 Eukaryotic translationinitiation factor 3 subunit G OS = Saccharomyces EIF3G_YEAST 30,501.6045 0 cerevisiae GN = TIF35 PE = 1 SV = 1 General transcriptionalcorepressor TUP1 OS = Saccharomyces TUP1_YEAST 78,307.20 45 0 cerevisiaeGN = TUP1 PE = 1 SV = 2 Heat shock protein 42 OS = Saccharomycescerevisiae GN = HSP42 HSP42_YEAST 42,817.50 44 0 PE = 1 SV = 1 60Sribosomal protein L15-B OS = Saccharomyces cerevisiae RL15B_YEAST24,422.60 84 1 GN = RPL15B PE = 1 SV = 2 40S ribosomal protein S23 OS =Saccharomyces cerevisiae RS23_YEAST 16,038.30 42 0 GN = RPS23A PE = 1 SV= 1 T-complex protein 1 subunit theta OS = Saccharomyces cerevisiaeTCPQ_YEAST 61,663.60 42 0 GN = CCT8 PE = 1 SV = 1 26S proteaseregulatory subunit 8 homolog OS = Saccharomyces PRS8_YEAST 45,272.60 410 cerevisiae GN = RPT6 PE = 1 SV = 4 SDO1-like protein YHR087W OS =Saccharomyces cerevisiae SDO1L_YEAST 12,009.80 41 0 GN = YHR087W PE = 1SV = 1 Mitochondrial escape protein 2 OS = Saccharomyces cerevisiaeYME2_YEAST 96,692.20 40 0 GN = YME2 PE = 1 SV = 1 Alpha-soluble NSFattachment protein OS = Saccharomyces cerevisiae SEC17_YEAST 32,804.4040 0 GN = SEC17 PE = 1 SV = 4 Protein translocation protein SEC63 OS =Saccharomyces cerevisiae SEC63_YEAST 75,348.10 40 0 GN = SEC63 PE = 1 SV= 2 Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrialPUT2_YEAST 64,437.50 40 0 OS = Saccharomyces cerevisiae GN = PUT2 PE = 1SV = 2 Polyamine N-acetyltransferase 1 OS = Saccharomyces cerevisiaePAA1_YEAST 21,948.70 79 1 GN = PAA1 PE = 1 SV = 1 40S ribosomal proteinS22-B OS = Saccharomyces cerevisiae RS22B_YEAST 14,626.50 79 1 GN =RPS22B PE = 1 SV = 3 Phosphoinositide phosphatase SAC1 OS =Saccharomyces cerevisiae SAC1_YEAST 71,125.90 38 0 GN = SAC1 PE = 1 SV =1 40S ribosomal protein S26-A OS = Saccharomyces cerevisiae RS26A_YEAST13,505.00 38 0 GN = RPS26A PE = 1 SV = 1 26S proteasome regulatorysubunit RPN2 OS = Saccharomyces RPN2_YEAST 104,237.00 76 1 cerevisiae GN= RPN2 PE = 1 SV = 4 Translational activator GCN1 OS = Saccharomycescerevisiae GCN1_YEAST 296,710.20 38 0 GN = GCN1 PE = 1 SV = 1Dolichyl-diphosphooligosaccharide--protein glycosyltransferaseSTT3_YEAST 81,532.90 38 0 subunit STT3 OS = Saccharomyces cerevisiae GN= STT3 PE = 1 SV = 2 1,3-beta-glucanosyltransferase GAS5 OS =Saccharomyces cerevisiae GAS5_YEAST 51,870.70 38 0 GN = GAS5 PE = 1 SV =1 Acyl-CoA-binding protein OS = Saccharomyces cerevisiae GN = ACB1ACBP_YEAST 10,061.80 38 0 PE = 1 SV = 3 Tricalbin-1 OS = Saccharomycescerevisiae GN = TCB1 PE = 1 SV = 1 TCB1_YEAST 133,581.30 37 0NADP-specific glutamate dehydrogenase 2 OS = Saccharomyces DHE5_YEAST49,627.60 37 0 cerevisiae GN = GDH3 PE = 1 SV = 1Dolichyl-phosphate-mannose--protein mannosyltransferase 1 PMT1_YEAST92,678.00 37 0 OS = Saccharomyces cerevisiae GN = PMT1 PE = 1 SV = 1Mitochondrial import inner membrane translocase subunit TIM10TIM10_YEAST 10,304.60 37 0 OS = Saccharomyces cerevisiae GN = MRS11 PE =1 SV = 1 Ornithine carbamoyltransferase OS = Saccharomyces cerevisiaeOTC_YEAST 37,846.40 37 0 GN = ARG3 PE = 1 SV = 1 Putativemagnesium-dependent phosphatase YER134C MGDP1_YEAST 20,442.40 36 0 OS =Saccharomyces cerevisiae GN = YER134C PE = 1 SV = 1 Eukaryotictranslation initiation factor 4B OS = Saccharomyces IF4B_YEAST 48,522.5036 0 cerevisiae GN = TIF3 PE = 1 SV = 1 Mitochondrial escape protein 2OS = Saccharomyces cerevisiae (strain YME2_YEAS7 96,662.30 36 0 YJM789)GN = YME2 PE = 3 SV = 1 Vesicle-associated membrane protein-associatedprotein SCS2 SCS2_YEAST 26,924.80 36 0 OS = Saccharomyces cerevisiae GN= SCS2 PE = 1 SV = 3 Importin beta SMX1 OS = Saccharomyces cerevisiae GN= SXM1 PE = 1 SXM1_YEAST 108,410.90 36 0 SV = 1 Inorganic phosphatetransport protein PHO88 OS = Saccharomyces PHO88_YEAST 21,138.00 36 0cerevisiae GN = PHO88 PE = 1 SV = 1 Transcription elongation factor SPT6OS = Saccharomyces cerevisiae SPT6_YEAST 168,298.50 71 1 GN = SPT6 PE =1 SV = 1 T-complex protein 1 subunit delta OS = Saccharomyces cerevisiaeTCPD_YEAST 57,605.60 35 0 GN = CCT4 PE = 1 SV = 2 5′-3′ exoribonuclease1 OS = Saccharomyces cerevisiae GN = KEM1 XRN1_YEAST 175,468.00 70 1 PE= 1 SV = 1 Fumarate reductase OS = Saccharomyces cerevisiae GN = YEL047CFRDS_YEAST 50,845.00 35 0 PE = 1 SV = 13-hydroxy-3-methylglutaryl-coenzyme A reductase 1 HMDH1_YEAST 115,629.1034 0 OS = Saccharomyces cerevisiae GN = HMG1 PE = 1 SV = 1 26Sproteasome regulatory subunit RPN9 OS = Saccharomyces RPN9_YEAST45,785.80 34 0 cerevisiae GN = RPN9 PE = 1 SV = 1Dolichyl-phosphate-mannose--protein mannosyltransferase 2 PMT2_YEAST86,872.80 34 0 OS = Saccharomyces cerevisiae GN = PMT2 PE = 1 SV = 2Bifunctional protein GAL10 OS = Saccharomyces cerevisiae GAL10_YEAST78,197.30 939 14 GN = GAL10 PE = 1 SV = 2 ATP-dependent bile acidpermease OS = Saccharomyces cerevisiae YBT1_YEAST 189,172.20 33 0 GN =YBT1 PE = 1 SV = 2 Saccharopine dehydrogenase [NAD+, L-lysine-forming]LYS1_YEAST 41,466.20 33 0 OS = Saccharomyces cerevisiae GN = LYS1 PE = 1SV = 3 Coatomer subunit gamma OS = Saccharomyces cerevisiae GN = SEC21COPG_YEAST 104,836.20 32 0 PE = 1 SV = 2 Cell division control protein53 OS = Saccharomyces cerevisiae CDC53_YEAST 93,949.60 32 0 GN = CDC53PE = 1 SV = 1 Rotenone-insensitive NADH-ubiquinone oxidoreductase,mitochondrial NDI1_YEAST 57,252.80 32 0 OS = Saccharomyces cerevisiae GN= NDI1 PE = 1 SV = 1 Argininosuccinate lyase OS = Saccharomycescerevisiae GN = ARG4 ARLY_YEAST 51,991.40 32 0 PE = 1 SV = 2 Zinc fingerprotein GIS2 OS = Saccharomyces cerevisiae GN = GIS2 GIS2_YEAST17,102.60 31 0 PE = 1 SV = 1 Protein kinase MCK1 OS = Saccharomycescerevisiae GN = MCK1 MCK1_YEAST 43,137.90 31 0 PE = 1 SV = 1 Malatedehydrogenase, peroxisomal OS = Saccharomyces cerevisiae MDHP_YEAST37,187.20 31 0 GN = MDH3 PE = 1 SV = 3 T-complex protein 1 subunit zetaOS = Saccharomyces cerevisiae TCPZ_YEAST 59,925.90 31 0 GN = CCT6 PE = 1SV = 1 ATP-dependent RNA helicase DBP2 OS = Saccharomyces cerevisiaeDBP2_YEAST 61,001.20 30 0 GN = DBP2 PE = 1 SV = 1 Cytochrome Bpre-mRNA-processing protein 6 OS = Saccharomyces CBP6_YEAST 18,679.70 300 cerevisiae GN = CBP6 PE = 1 SV = 1 Protein DCS2 OS = Saccharomycescerevisiae GN = DCS2 PE = 1 SV = 3 DCS2_YEAST 40,941.80 30 0 Eukaryotictranslation initiation factor 3 subunit A OS = Saccharomyces EIF3A_YEAST110,348.50 176 3 cerevisiae GN = TIF32 PE = 1 SV = 1 Glucose-signalingfactor 2 OS = Saccharomyces cerevisiae GN = GSF2 GSF2_YEAST 45,872.50 581 PE = 1 SV = 1 Glycerol-3-phosphate dehydrogenase [NAD+] 2,mitochondrial GPD2_YEAST 49,422.10 29 0 OS = Saccharomyces cerevisiae GN= GPD2 PE = 1 SV = 2 Prohibitin-2 OS = Saccharomyces cerevisiae GN =PHB2 PE = 1 SV = 2 PHB2_YEAST 34,407.20 29 0 40S ribosomal protein S29-AOS = Saccharomyces cerevisiae RS29A_YEAST 6,660.70 29 0 GN = RPS29A PE =1 SV = 3 DNA-directed RNA polymerase I subunit RPA1 OS = SaccharomycesRPA1_YEAST 186,435.30 29 0 cerevisiae GN = RPA1 PE = 1 SV = 2 Proteintransport protein SEC24 OS = Saccharomyces cerevisiae SEC24_YEAST103,638.70 29 0 GN = SEC24 PE = 1 SV = 1 Carboxypeptidase Y OS =Saccharomyces cerevisiae GN = PRC1 PE = 1 CBPY_YEAST 59,803.60 28 0 SV =1 V-type proton ATPase subunit d OS = Saccharomyces cerevisiaeVA0D_YEAST 39,792.40 28 0 GN = VMA6 PE = 1 SV = 2 Uncharacterizedprotein YJL171C OS = Saccharomyces cerevisiae YJR1_YEAST 43,014.50 28 0GN = YJL1710 PE = 1 SV = 1 Vacuolar protein sorting/targeting proteinPEP1 OS = Saccharomyces PEP1_YEAST 177,783.50 28 0 cerevisiae GN = PEP1PE = 1 SV = 1 FACT complex subunit POB3 OS = Saccharomyces cerevisiaePOB3_YEAST 62,995.20 28 0 GN = POB3 PE = 1 SV = 1 Uncharacterizedmitochondrial membrane protein FMP10 FMP10_YEAST 27,698.90 28 0 OS =Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1 RNA annealing proteinYRA1 OS = Saccharomyces cerevisiae YRA1_YEAST 24,956.30 27 0 GN = YRA1PE = 1 SV = 2 Mitochondrial outer membrane protein OM45 OS =Saccharomyces OM45_YEAST 44,582.00 27 0 cerevisiae GN = OM45 PE = 1 SV =2 Mitochondrial import receptor subunit TOM5 OS = SaccharomycesTOM5_YEAST 5,984.70 27 0 cerevisiae GN = TOM5 PE = 1 SV = 1 T-complexprotein 1 subunit alpha OS = Saccharomyces cerevisiae TCPA_YEAST60,482.30 27 0 GN = TCP1 PE = 1 SV = 2 Eukaryotic translation initiationfactor lA OS = Saccharomyces IF1A_YEAST 17,435.70 26 0 cerevisiae GN =TIF11 PE = 1 SV = 1 Protein MSN5 OS = Saccharomyces cerevisiae GN = MSN5PE = 1 SV = 1 MSN5_YEAST 142,126.30 26 0 Putative fatty aldehydedehydrogenase HFD1 OS = Saccharomyces HFD1_YEAST 59,981.90 26 0cerevisiae GN = HFD1 PE = 1 SV = 1 Ergosterol biosynthetic protein 28 OS= Saccharomyces cerevisiae ERG28_YEAST 17,135.80 26 0 GN = ERG28 PE = 1SV = 1 Protein YRO2 OS = Saccharomyces cerevisiae GN = YRO2 PE = 1 SV =1 YRO2_YEAST 38,721.30 26 0 Methylene-fatty-acyl-phospholipid synthaseOS = Saccharomyces PEM2_YEAST 23,151.10 26 0 cerevisiae GN = PEM2 PE = 1SV = 1 Protein MKT1 OS = Saccharomyces cerevisiae GN = MKT1 PE = 1 SV =2 MKT1_YEAST 94,499.40 25 0 Protein MRH1 OS = Saccharomyces cerevisiaeGN = MRH1 PE = 1 SV = 1 MRH1_YEAST 36,192.40 25 0 Eukaryotic translationinitiation factor 2 subunit beta IF2B_YEAST 31,575.70 25 0 OS =Saccharomyces cerevisiae GN = SUI3 PE = 1 SV = 2 Peroxiredoxin TSA2 OS =Saccharomyces cerevisiae GN = TSA2 PE = 1 TSA2_YEAST 21,615.40 24 0 SV =3 Endoplasmic reticulum vesicle protein 25 OS = SaccharomycesTMEDA_YEAST 24,106.40 24 0 cerevisiae GN = ERV25 PE = 1 SV = 1 PKHD-typehydroxylase TPA1 OS = Saccharomyces cerevisiae TPA1_YEAST 74,044.60 24 0GN = TPA1 PE = 1 SV = 1 SED5-binding protein 3 OS = Saccharomycescerevisiae GN = SFB3 SFB3_YEAST 103,953.30 24 0 PE = 1 SV = 1 D-lactatedehydrogenase [cytochrome] 3 OS = Saccharomyces DLD3_YEAST 55,226.80 240 cerevisiae GN = DLD3 PE = 1 SV = 1 Single-stranded nucleicacid-binding protein OS = Saccharomyces SSBP1_YEAST 32,989.90 47 1cerevisiae GN = SBP1 PE = 1 SV = 2 Protein CW H43 OS = Saccharomycescerevisiae GN = CW H43 PE = 1 CWH43_YEAST 107,887.70 23 0 SV = 2T-complex protein 1 subunit eta OS = Saccharomyces cerevisiae TCPH_YEAST59,737.10 23 0 GN = CCT7 PE = 1 SV = 1 26S protease regulatory subunit6B homolog OS = Saccharomyces PRS6B_YEAST 47,971.50 23 0 cerevisiae GN =RPT3 PE = 1 SV = 1 NADH-cytochrome b5 reductase 1 OS = Saccharomycescerevisiae NCB5R_YEAST 31,494.80 23 0 GN = CBR1 PE = 1 SV = 2 Glycogendebranching enzyme OS = Saccharomyces cerevisiae GDE_YEAST 174,978.70 461 GN = GDB1 PE = 1 SV = 1 C-5 sterol desaturase OS = Saccharomycescerevisiae GN = ERG3 ERG3_YEAST 42,731.70 23 0 PE = 1 SV = 1 13 kDaribonucleoprotein-associated protein OS = Saccharomyces SNU13_YEAST13,569.40 23 0 cerevisiae GN = SNU13 PE = 1 SV = 1 UPF0202 protein KRE33OS = Saccharomyces cerevisiae GN = KRE33 KRE33_YEAST 119,353.80 23 0 PE= 1 SV = 1 Protein phosphatase PP2A regulatory subunit A OS =Saccharomyces 2AAA_YEAST 70,954.70 23 0 cerevisiae GN = TPD3 PE = 1 SV =2 Eukaryotic translation initiation factor 2 subunit gamma IF2G_YEAST57,867.20 23 0 OS = Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1Midasin OS = Saccharomyces cerevisiae GN = MDN1 PE = 1 SV = 1 MDN1_YEAST559,323.50 23 0 Galactose-1-phosphate uridylyltransferase OS =Saccharomyces GAL7_YEAST 42,386.00 459 10 cerevisiae GN = GAL7 PE = 1 SV= 4 UPF0121 membrane protein YLL023C OS = Saccharomyces cerevisiaeYL023_YEAST 32,187.70 22 0 GN = YLL023C PE = 1 SV = 1Phosphatidylinositol transfer protein PDR16 OS = SaccharomycesPDR16_YEAST 40,715.80 22 0 cerevisiae GN = PDR16 PE = 1 SV = 1 60Sribosomal protein L43 OS = Saccharomyces cerevisiae RL43_YEAST 10,090.8022 0 GN = RPL43A PE = 1 SV = 2 Arginine biosynthesis bifunctionalprotein ARG7, mitochondrial ARGJ_YEAST 47,850.20 22 0 OS = Saccharomycescerevisiae GN = ARG7 PE = 1 SV = 1 Probable family 17 glucosidase SCW4OS = Saccharomyces cerevisiae SCW4_YEAST 40,172.20 22 0 GN = SCW4 PE = 1SV = 1 26S protease subunit RPT4 OS = Saccharomyces cerevisiaePRS10_YEAST 49,410.10 22 0 GN = RPT4 PE = 1 SV = 4 60S ribosomal proteinL3 OS = Saccharomyces cerevisiae GN = RPL3 RL3_YEAST 43,757.90 219 5 PE= 1 SV = 4 Phosphoglucomutase-2 OS = Saccharomyces cerevisiae GN = PGM2PGM2_YEAST 63,091.20 345 8 PE = 1 SV = 1 Uncharacterized phosphataseYNL010W OS = Saccharomyces YNB0_YEAST 27,481.40 43 1 cerevisiae GN =YNL010W PE = 1 SV = 1 Elongation factor 3A OS = Saccharomyces cerevisiaeGN = YEF3 PE = 1 EF3A_YEAST 115,996.20 892 21 SV = 3 Casein kinase IIsubunit alpha′ OS = Saccharomyces cerevisiae CSK22_YEAST 39,405.00 21 0GN = CKA2 PE = 1 SV = 2 54S ribosomal protein L12, mitochondrial OS =Saccharomyces MNP1_YEAST 20,650.80 21 0 cerevisiae GN = MNP1 PE = 1 SV =1 Nuclear protein SNF4 OS = Saccharomyces cerevisiae GN = SNF4SNF4_YEAST 36,402.50 21 0 PE = 1 SV = 1 Eukaryotic initiation factor 4Fsubunit p150 OS = Saccharomyces IF4F1_YEAST 107,103.80 21 0 cerevisiaeGN = TIF4631 PE = 1 SV = 2 Medium-chain fatty acid ethyl estersynthase/esterase 2 MCFS2_YEAST 51,256.90 21 0 OS = Saccharomycescerevisiae GN = EHT1 PE = 1 SV = 1 ABC transporter ATP-binding proteinARB1 OS = Saccharomyces ARB1_YEAST 68,379.50 21 0 cerevisiae GN = ARB1PE = 1 SV = 1 Cysteinyl-tRNA synthetase OS = Saccharomyces cerevisiae GN= YNL247W PE = 1 SV = 1 SYC_YEAST 87,533.90 21 0 Protein TTP1 OS =Saccharomyces cerevisiae GN = TTP1 PE = 1 SV = 1 TTP1_YEAST 67,777.60 210 26S proteasome regulatory subunit RPN8 OS = Saccharomyces RPN8_YEAST38,313.90 21 0 cerevisiae GN = RPN8 PE = 1 SV = 3 NADH-cytochrome b5reductase 1 OS = Saccharomyces cerevisiae NCB5R_YEAS7 31,422.60 21 0(strain YJM789) GN = CBR1 PE = 2 SV = 2 ER membrane protein complexsubunit 1 OS = Saccharomyces EMC1_YEAST 87,185.00 21 0 cerevisiae GN =EMC1 PE = 1 SV = 1 Heat shock protein 78, mitochondrial OS =Saccharomyces cerevisiae HSP78_YEAST 91,340.80 292 7 GN = HSP78 PE = 1SV = 2 Nuclear protein STH1/NPS1 OS = Saccharomyces cerevisiaeSTH1_YEAST 156,750.60 20 0 GN = STH1 PE = 1 SV = 1 mRNA-binding proteinPUF3 OS = Saccharomyces cerevisiae PUF3_YEAST 98,070.00 20 0 GN = PUF3PE = 1 SV = 1 Actin-interacting protein 1 OS = Saccharomyces cerevisiaeGN = AIP1 AIP1_YEAST 67,326.00 20 0 PE = 1 SV = 1 Cytochrome c iso-1 OS= Saccharomyces cerevisiae GN = CYC1 PE = 1 CYC1_YEAST 12,182.50 80 2 SV= 2 CTP synthase 1 OS = Saccharomyces cerevisiae GN = URA7 PE = 1URA7_YEAST 64,711.50 20 0 SV = 2 Squalene monooxygenase OS =Saccharomyces cerevisiae GN = ERG1 ERG1_YEAST 55,127.20 20 0 PE = 1 SV =2 Putative aldehyde dehydrogenase-like protein YHR039C MSC7_YEAST71,322.60 20 0 OS = Saccharomyces cerevisiae GN = MSC7 PE = 1 SV = 1Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]GFA1_YEAST 80,048.70 78 2 OS = Saccharomyces cerevisiae GN = GFA1 PE = 1SV = 4 Uncharacterized GTP-binding protein OLA1 OS = SaccharomycesOLA1_YEAST 44,175.90 155 4 cerevisiae GN = OLA1 PE = 1 SV = 1 Probable1-acyl-sn-glycerol-3-phosphate acyltransferase PLSC_YEAST 33,887.80 19 0OS = Saccharomyces cerevisiae GN = SLC1 PE = 1 SV = 1Sporulation-specific protein 21 OS = Saccharomyces cerevisiaeMPC70_YEAST 69,881.80 19 0 GN = SPO21 PE = 1 SV = 1 Cell divisioncontrol protein 42 OS = Saccharomyces cerevisiae CDC42_YEAST 21,322.6019 0 GN = CDC42 PE = 1 SV = 2 Serine/threonine-protein phosphatase PP-Z2OS = Saccharomyces PPZ2_YEAST 78,494.20 19 0 cerevisiae GN = PPZ2 PE = 1SV = 4 Putative mitochondrial carrier protein YHM1/SHM1 YHM1_YEAST33,217.70 19 0 OS = Saccharomyces cerevisiae GN = YHM1 PE = 1 SV = 1 60Sribosomal protein L24-A OS = Saccharomyces cerevisiae RL24A_YEAST17,614.40 38 1 GN = RPL24A PE = 1 SV = 1 60S ribosomal protein L35 OS =Saccharomyces cerevisiae RL35_YEAST 13,910.20 38 1 GN = RPL35A PE = 1 SV= 1 Mitochondrial respiratory chain complexes assembly protein RCA1RCA1_YEAST 93,280.10 19 0 OS = Saccharomyces cerevisiae GN = RCA1 PE = 1SV = 2 Prohibitin-1 OS = Saccharomyces cerevisiae GN = PHB1 PE = 1 SV =2 PHB1_YEAST 31,427.90 38 1 T-complex protein 1 subunit epsilon OS =Saccharomyces cerevisiae TCPE_YEAST 61,916.50 19 0 GN = CCT5 PE = 1 SV =3 Translation machinery-associated protein 22 OS = SaccharomycesDENR_YEAS7 22,495.70 19 0 cerevisiae (strain YJM789) GN = TMA22 PE = 3SV = 1 (+1) DnaJ homolog 1, mitochondrial OS = Saccharomyces cerevisiaeMDJ1_YEAST 55,562.00 19 0 GN = MDJ1 PE = 1 SV = 1Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 56 kDa TPS1_YEAST56,148.30 76 2 subunit OS = Saccharomyces cerevisiae GN = TPS1 PE = 1 SV= 2 Acetyl-coenzyme A synthetase 2 OS = Saccharomyces cerevisiaeACS2_YEAST 75,492.20 228 6 GN = ACS2 PE = 1 SV = 1 60S ribosomal proteinL24-B OS = Saccharomyces cerevisiae RL24B_YEAST 17,548.10 38 1 GN =RPL24B PE = 1 SV = 1 Protein YGP1 OS = Saccharomyces cerevisiae GN =YGP1 PE = 1 SV = 2 YGP1_YEAST 37,328.10 19 0 Actin-related protein 2/3complex subunit 3 OS = Saccharomyces ARPC3_YEAST 20,579.60 19 0cerevisiae GN = ARC18 PE = 1 SV = 1 Isoleucyl-tRNA synthetase,cytoplasmic OS = Saccharomyces SYIC_YEAST 122,988.30 262 7 cerevisiae GN= ILS1 PE = 1 SV = 1 Eukaryotic translation initiation factor 3 subunit10S = Saccharomyces EIF3I_YEAS7 38,756.20 37 1 cerevisiae (strainYJM789) GN = TIF34 PE = 3 SV = 1 (+1) Dolichol-phosphatemannosyltransferase OS = Saccharomyces DPM1_YEAST 30,363.40 73 2cerevisiae GN = DPM1 PE = 1 SV = 3 40S ribosomal protein S29-B OS =Saccharomyces cerevisiae RS29B_YEAST 6,727.60 18 0 GN = RPS29B PE = 1 SV= 3 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43PRP43_YEAST 87,564.80 18 0 OS = Saccharomyces cerevisiae GN = PRP43 PE =1 SV = 1 Translocation protein SEC72 OS = Saccharomyces cerevisiaeSEC72_YEAST 21,608.40 18 0 GN = SEC72 PE = 1 SV = 3 Transcriptionelongation factor SPT5 OS = Saccharomyces cerevisiae SPT5_YEAST115,651.40 36 1 GN = SPT5 PE = 1 SV = 1 Endoplasmic reticulumtransmembrane protein 1 OS = Saccharomyces YET1_YEAST 23,428.60 18 0cerevisiae GN = YET1 PE = 1 SV = 1 Ferrochelatase, mitochondrial OS =Saccharomyces cerevisiae HEMH_YEAST 44,597.70 18 0 GN = HEM15 PE = 1 SV= 1 Protein CBP3, mitochondrial OS = Saccharomyces cerevisiae CBP3_YEAST39,085.40 18 0 GN = CBP3 PE = 1 SV = 1 Putative proteindisulfide-isomerase YIL005W OS = Saccharomyces YIA5_YEAST 81,223.80 18 0cerevisiae GN = YIL005W PE = 1 SV = 1 Mitochondrial protein importprotein MASS OS = Saccharomyces MASS _YEAST 44,671.70 72 2 cerevisiae GN= YDJ1 PE = 1 SV = 1 Peroxisomal-coenzyme A synthetase OS =Saccharomyces cerevisiae FAT2_YEAST 60,489.90 18 0 GN = FAT2 PE = 1 SV =1 Nuclear cap-binding protein complex subunit 1 OS = SaccharomycesNCBP1_YEAST 100,023.30 36 1 cerevisiae GN = STO1 PE = 1 SV = 2Proteasome component Y13 OS = Saccharomyces cerevisiae PSA4_YEAST28,715.80 18 0 GN = PRE9 PE = 1 SV = 1 Trehalose synthase complexregulatory subunit TSL1 TSL1_YEAST 123,021.70 70 2 OS = Saccharomycescerevisiae GN = TSL1 PE = 1 SV = 1 Ribosomal RNA-processing protein 12OS = Saccharomyces cerevisiae RRP12_YEAST 137,515.10 17 0 GN = RRP12 PE= 1 SV = 1 U3 small nucleolar RNA-associated protein 22 OS =Saccharomyces UTP22_YEAST 140,492.90 17 0 cerevisiae GN = UTP22 PE = 1SV = 1 40S ribosomal protein S26-B OS = Saccharomyces cerevisiaeRS26B_YEAST 13,447.00 34 1 GN = RPS26B PE = 1 SV = 1 Elongator complexprotein 1 OS = Saccharomyces cerevisiae GN = IKI3 ELP1_YEAST 152,994.2017 0 PE = 1 SV = 1 Probable 1,3-beta-glucanosyltransferase GAS3 OS =Saccharomyces GAS3_YEAST 56,796.00 17 0 cerevisiae GN = GAS3 PE = 1 SV =1 Dynamin-related protein DNM1 OS = Saccharomyces cerevisiae DNM1_YEAST84,976.60 68 2 GN = DNM1 PE = 1 SV = 1 Pyruvate dehydrogenase complexprotein X component, mitochondrial ODPX_YEAST 45,363.80 34 1 OS =Saccharomyces cerevisiae GN = PDX1 PE = 1 SV = 1 GTP-binding proteinRHO3 OS = Saccharomyces cerevisiae GN = RHO3 RHO3_YEAST 25,312.80 17 0PE = 1 SV = 2 DNA-directed RNA polymerase I subunit RPA2 OS =Saccharomyces RPA2_YEAST 135,745.40 33 1 cerevisiae GN = RPA2 PE = 1 SV= 1 54S ribosomal protein YmL6, mitochondrial OS = SaccharomycesRL4P_YEAST 31,970.50 16 0 cerevisiae GN = YML6 PE = 1 SV = 1 ER-derivedvesicles protein ERV29 OS = Saccharomyces cerevisiae ERV29_YEAST35,014.90 16 0 GN = ERV29 PE = 1 SV = 1 54S ribosomal protein L3,mitochondrial OS = Saccharomyces RM03_YEAST 44,001.20 16 0 cerevisiae GN= MRPL3 PE = 1 SV = 2 Pyrroline-5-carboxylate reductase OS =Saccharomyces cerevisiae P5CR_YEAST 30,131.40 16 0 GN = PRO3 PE = 1 SV =1 60S ribosomal protein L34-A OS = Saccharomyces cerevisiae RL34A_YEAST13,639.20 16 0 GN = RPL34A PE = 1 SV = 1 (+1) Serine/threonine-proteinkinase YPK1 OS = Saccharomyces cerevisiae YPK1_YEAST 76,483.80 16 0 GN =YPK1 PE = 1 SV = 2 60S ribosomal protein L19 OS = Saccharomycescerevisiae RL19_YEAST 21,704.60 32 1 GN = RPL19A PE = 1 SV = 5CDP-diacylglycerol--inositol 3-phosphatidyltransferase PIS_YEAST24,824.30 16 0 OS = Saccharomyces cerevisiae GN = PIS1 PE = 1 SV = 1 60Sribosome subunit biogenesis protein NIP7 OS = Saccharomyces NIP7_YEAST20,381.10 16 0 cerevisiae GN = NIP7 PE = 1 SV = 1 Cell division controlprotein 10 OS = Saccharomyces cerevisiae CDC10_YEAST 37,026.30 16 0 GN =CDC10 PE = 1 SV = 1 E3 ubiquitin-protein ligase RSP5 OS = Saccharomycescerevisiae RSP5_YEAST 91,817.40 16 0 GN = RSP5 PE = 1 SV = 1 Glucan1,3-beta-glucosidase I/II OS= Saccharomyces cerevisiae EXG1_YEAST51,312.30 16 0 GN = EXG1 PE = 1 SV = 1 Eukaryotic translation initiationfactor 5A-2 OS = Saccharomyces IF5A2_YEAST 17,114.60 346 11 cerevisiaeGN = HYP2 PE = 1 SV = 3 1,4-alpha-glucan-branching enzyme OS =Saccharomyces cerevisiae GLGB_YEAST 81,118.50 31 1 GN = GLC3 PE = 1 SV =2 Polyadenylate-binding protein, cytoplasmic and nuclear PABP_YEAST64,345.40 183 6 OS = Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4Protein GCY OS = Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1GCY_YEAST 35,079.90 272 9 Putative thiosulfate sulfurtransferase YOR285WOS = Saccharomyces YO285 _YEAST 15,413.30 30 1 cerevisiae GN = YOR285WPE = 1 SV = 1 DNA topoisomerase 2-associated protein PAT1 OS =Saccharomyces PAT1_YEAST 88,499.40 15 0 cerevisiae GN = PAT1 PE = 1 SV =3 CAAX prenyl protease 1 OS = Saccharomyces cerevisiae GN = STE24STE24_YEAST 52,327.50 15 0 PE = 1 SV = 1 Endoplasmic reticulumtransmembrane protein 3 OS = Saccharomyces YET3_YEAST 22,904.20 15 0cerevisiae GN = YET3 PE = 1 SV = 1 ATP-dependent RNA helicase DOB1 OS =Saccharomyces cerevisiae MTR4_YEAST 122,058.70 15 0 GN = MTR4 PE = 1 SV= 1 Translation machinery-associated protein 17 OS = SaccharomycesTMA17_YEAST 16,771.90 15 0 cerevisiae GN = TMA17 PE = 1 SV = 1 Carboncatabolite-derepressing protein kinase OS = Saccharomyces SNF1_YEAST72,047.90 15 0 cerevisiae GN = SNF1 PE = 1 SV = 1 tRNA(cytosine-5-)-methyltransferase NCL1 OS = Saccharomyces NCL1_YEAST77,879.60 15 0 cerevisiae GN = NCL1 PE = 1 SV = 1 Protein transportprotein SEC61 OS = Saccharomyces cerevisiae SC61A_YEAST 52,940.20 15 0GN = SEC61 PE = 1 SV = 1 Calcineurin subunit B OS = Saccharomycescerevisiae GN = CNB1 PE = 1 SV = 3 CANB_YEAST 19,640.10 15 0Lysophospholipase 1 OS = Saccharomyces cerevisiae GN = PLB1 PE = 1PLB1_YEAST 71,670.00 15 0 SV = 2 Proteasome component Y7 OS =Saccharomyces cerevisiae GN = PRE8 PSA2_YEAST 27,163.10 15 0 PE = 1 SV =1 Metal resistance protein YCF1 OS = Saccharomyces cerevisiae YCF1_YEAST171,129.30 15 0 GN = YCF1 PE = 1 SV = 2 Ran GTPase-activating protein 1OS = Saccharomyces cerevisiae GN = RNA1 PE = 1 SV = 2 RNAL_YEAST45,817.80 15 0 L-aminoadipate-semialdehyde dehydrogenase OS =Saccharomyces LYS2_YEAST 155,350.80 30 1 cerevisiae GN = LYS2 PE = 1 SV= 2 Serine hydroxymethyltransferase, mitochondrial OS = SaccharomycesGLYM_YEAST 53,688.00 30 1 cerevisiae GN = SHM1 PE = 1 SV = 2 Coatomersubunit alpha OS = Saccharomyces cerevisiae GN = RET1 COPA_YEAST135,611.20 89 3 PE = 1 SV = 2 40S ribosomal protein S10-B OS =Saccharomyces cerevisiae GN = RPS10B PE = 1 SV = 1 RS10B_YEAST 12,738.7089 3 40S ribosomal protein S10-A OS = Saccharomyces cerevisiaeRS10A_YEAST 12,739.70 89 3 GN = RPS10A PE = 1 SV = 1 Tryptophan synthaseOS = Saccharomyces cerevisiae GN = TRP5 PE = 1 TRP_YEAST 76,626.60 59 2SV = 1 Serine/threonine-protein phosphatase PP1-2 OS = SaccharomycesPP12_YEAST 35,909.00 58 2 cerevisiae GN = GLC7 PE = 1 SV = 1Aminopeptidase Y OS = Saccharomyces cerevisiae GN = APE3 PE = 1APE3_YEAST 60,139.20 29 1 SV = 1 Glycerol-3-phosphate dehydrogenase[NAD+] 1 OS = Saccharomyces GPD1_YEAST 42,868.60 115 4 cerevisiae GN =GPD1 PE = 1 SV = 4 Valyl-tRNA synthetase, mitochondrial OS =Saccharomyces cerevisiae SYV_YEAST 125,774.70 172 6 GN = VAS1 PE = 1 SV= 2 Aconitate hydratase, mitochondrial OS = Saccharomyces cerevisiaeACON_YEAST 85,371.60 688 24 GN = ACO1 PE = 1 SV = 2 Elongation factorTu, mitochondrial OS = Saccharomyces cerevisiae EFTU_YEAST 47,972.90 572 GN = TUF1 PE = 1 SV = 1 Glycerol-3-phosphate 0-acyltransferase 2 OS =Saccharomyces GPT2_YEAST 83,648.60 14 0 cerevisiae GN = GPT2 PE = 1 SV =1 Putative ribosomal RNA methyltransferase Nop2 OS = SaccharomycesNOP2_YEAST 69,814.30 14 0 cerevisiae GN = NOP2 PE = 1 SV = 1Serine/threonine-protein kinase YPK2/YKR2 OS = Saccharomyces YPK2_YEAST76,669.00 14 0 cerevisiae GN = YPK2 PE = 1 SV = 1 Xanthinephosphoribosyltransferase 1 OS = Saccharomyces cerevisiae XPT1_YEAST23,672.00 14 0 GN = XPT1 PE = 1 SV = 13-hydroxy-3-methylglutaryl-coenzyme A reductase 2 HMDH2_YEAST 115,696.9014 0 OS = Saccharomyces cerevisiae GN = HMG2 PE = 1 SV = 13-keto-steroid reductase OS = Saccharomyces cerevisiae GN = ERG27ERG27_YEAST 39,726.60 14 0 PE = 1 SV = 1 Ras-like protein 2 OS =Saccharomyces cerevisiae GN = RAS2 PE = 1 RAS2_YEAST 34,705.00 14 0 SV =4 Protein phosphatase 1 regulatory subunit SDS22 OS = SaccharomycesSDS22_YEAST 38,890.20 14 0 cerevisiae GN = SDS22 PE = 1 SV = 1Ubiquitin-like protein SMT3 OS = Saccharomyces cerevisiae GN = SMT3SMT3_YEAST 11,597.50 28 1 PE = 1 SV = 1 Sphingosine-1-phosphate lyase OS= Saccharomyces cerevisiae SGPL_YEAST 65,567.50 14 0 GN = DPL1 PE = 1 SV= 1 Protein transport protein SSS1 OS = Saccharomyces cerevisiaeSC61G_YEAST 8,943.80 14 0 GN = SSS1 PE = 1 SV = 2 UPF0674 endoplasmicreticulum membrane protein YNR021W YN8B_YEAST 47,095.10 14 0 OS =Saccharomyces cerevisiae GN = YNR021W PE = 1 SV = 3 Non-classical exportprotein 2 OS = Saccharomyces cerevisiae NCE2_YEAST 18,967.70 14 0 GN =NCE102 PE = 1 SV = 1 Reduced viability upon starvation protein 161 OS =Saccharomyces RV161_YEAST 30,251.90 14 0 cerevisiae GN = RVS161 PE = 1SV = 1 Cytochrome b5 OS = Saccharomyces cerevisiae GN = CYB5 PE = 1CYB5_YEAST 13,297.10 14 0 SV = 2 60S ribosomal protein L37-A OS =Saccharomyces cerevisiae RL37A_YEAST 9,850.40 14 0 GN = RPL37A PE = 1 SV= 2 Calmodulin OS = Saccharomyces cerevisiae GN = CMD1 PE = 1 SV = 1CALM_YEAST 16,135.50 14 0 Actin-related protein 2/3 complex subunit 5 OS= Saccharomyces ARPC5_YEAST 17,134.60 14 0 cerevisiae GN = ARC15 PE = 1SV = 1 Mitochondrial outer membrane protein SCY_3392 YKR18_YEAS781,773.40 14 0 OS = Saccharomyces cerevisiae (strain YJM789) GN =SCY_3392 PE = 3 (+1) SV = 1 tRNA pseudouridine synthase 1 OS =Saccharomyces cerevisiae PUS1_YEAST 62,145.30 14 0 GN = PUS1 PE = 1 SV =1 Heterotrimeric G protein gamma subunit GPG1 OS = SaccharomycesGPG1_YEAST 14,922.30 14 0 cerevisiae GN = GPG1 PE = 1 SV = 1Anthranilate synthase component 1 OS = Saccharomyces cerevisiaeTRPE_YEAST 56,769.50 14 0 GN = TRP2 PE = 1 SV = 4 UPF0662 proteinYPL260W OS = Saccharomyces cerevisiae YP260_YEAST 62,782.70 27 1 GN =YPL260W PE = 1 SV = 1 NADPH-dependent 1-acyldihydroxyacetone phosphatereductase AYR1_YEAST 32,815.30 27 1 OS = Saccharomyces cerevisiae GN =AYR1 PE = 1 SV = 1 Long-chain-fatty-acid--CoA ligase 1 OS =Saccharomyces cerevisiae LCF1_YEAST 77,868.10 81 3 GN = FAA1 PE = 1 SV =1 Small COPII coat GTPase SAR10S = Saccharomyces cerevisiae SAM_YEAST21,451.50 53 2 GN = SAR1 PE = 1 SV = 1 GMP synthase[glutamine-hydrolyzing] OS = Saccharomyces cerevisiae GUAA_YEAST58,483.40 53 2 GN = GUA1 PE = 1 SV = 4 Mitochondrial outer membraneprotein porin 1 OS = Saccharomyces VDAC1_YEAST 30,429.50 185 7cerevisiae GN = POR1 PE = 1 SV = 4 ATP-dependent helicase NAM7 OS =Saccharomyces cerevisiae NAM7_YEAST 109,432.60 13 0 GN = NAM7 PE = 1 SV= 1 Proteasome component PRE2 OS = Saccharomyces cerevisiae PSB5_YEAST31,636.90 13 0 GN = PRE2 PE = 1 SV = 3 Homocitrate synthase,mitochondrial OS = Saccharomyces cerevisiae HOSM_YEAST 48,595.50 78 3 GN= LYS21 PE = 1 SV = 1 Nucleolar complex protein 2 OS = Saccharomycescerevisiae NOC2_YEAST 81,605.10 13 0 GN = NOC2 PE = 1 SV = 2Transcriptional regulatory protein SIN3 OS = Saccharomyces cerevisiaeSIN3_YEAST 174,843.10 13 0 GN = SIN3 PE = 1 SV = 2 Ribosome biogenesisprotein ERB1 OS = Saccharomyces cerevisiae ERB1_YEAS7 91,706.30 13 0(strain YJM789) GN = ERB1 PE = 3 SV = 1 (+1) Dihydroxy-acid dehydratase,mitochondrial OS = Saccharomyces ILV3_YEAST 62,862.80 78 3 cerevisiae GN= ILV3 PE = 1 SV = 2 Uncharacterized protein YKL054C OS = Saccharomycescerevisiae YKF4_YEAST 83,968.30 13 0 GN = YKL054C PE = 1 SV = 1DNA-directed RNA polymerases I, II, and III subunit RPABC5 RPAB5_YEAST8,278.00 13 0 OS = Saccharomyces cerevisiae GN = RPB10 PE = 1 SV = 2Mitochondrial presequence protease OS = Saccharomyces cerevisiaeCYM1_YEAST 112,185.50 26 1 GN = CYM1 PE = 1 SV = 2Amidophosphoribosyltransferase OS = Saccharomyces cerevisiae PUR1_YEAST56,720.30 13 0 GN = ADE4 PE = 1 SV = 2 Protein ERP1 OS = Saccharomycescerevisiae GN = ERP1 PE = 1 SV = 1 ERP1_YEAST 24,724.00 13 0 Hsp90co-chaperone HCH1 OS = Saccharomyces cerevisiae HCH1_YEAST 17,246.80 130 GN = HCH1 PE = 1 SV = 1 Acetyl-CoA carboxylase OS = Saccharomycescerevisiae GN = FAS3 ACAC_YEAST 250,359.50 572 22 PE = 1 SV = 2Mitochondrial outer membrane protein IML2 OS = Saccharomyces IML2_YEAS782,553.00 13 0 cerevisiae (strain YJM789) GN = IML2 PE = 3 SV = 1 (+1)Choline-phosphate cytidylyltransferase OS = Saccharomyces cerevisiaePCY1_YEAST 49,408.40 13 0 GN = PCT1 PE = 1 SV = 2 Nucleosome assemblyprotein OS = Saccharomyces cerevisiae NAP1_YEAST 47,886.10 13 0 GN =NAP1 PE = 1 SV = 2 THO complex subunit 2 OS = Saccharomyces cerevisiaeGN = THO2 THO2_YEAST 183,940.50 13 0 PE = 1 SV = 1 Sec sixty-one proteinhomolog OS = Saccharomyces cerevisiae SSH1_YEAST 53,314.50 13 0 GN =SSH1 PE = 1 SV = 1 Cytochrome c heme lyase OS = Saccharomyces cerevisiaeGN = CYC3 CCHL_YEAST 30,080.70 13 0 PE = 1 SV = 1 Prefoldin subunit 4 OS= Saccharomyces cerevisiae GN = GIM3 PE = 1 PFD4_YEAST 15,181.00 13 0 SV= 1 Gamma-glutamyl phosphate reductase OS = Saccharomyces PROA_YEAST49,742.20 13 0 cerevisiae GN = PRO2 PE = 1 SV = 1 60S ribosomal proteinL37-B OS = Saccharomyces cerevisiae RL37B_YEAST 9,868.30 13 0 GN =RPL37B PE = 1 SV = 2 UPF0368 protein YPL225W OS = Saccharomycescerevisiae YP225_YEAST 17,445.20 26 1 GN = YPL225W PE = 1 SV = 1Dolichyl-phosphate-mannose--protein mannosyltransferase 4 PMT4_YEAST87,968.60 13 0 OS = Saccharomyces cerevisiae GN = PMT4 PE = 1 SV = 1Increased sodium tolerance protein 2 OS = Saccharomyces cerevisiaeIST2_YEAST 105,908.10 13 0 GN = IST2 PE = 1 SV = 1 Glucokinase-1 OS =Saccharomyces cerevisiae GN = GLK1 PE = 1 SV = 1 HXKG_YEAST 55,379.10231 9 Suppressor protein STM1 OS = Saccharomyces cerevisiae GN = STM1STM1_YEAST 29,995.40 202 8 PE = 1 SV = 3 Uridylate kinase OS =Saccharomyces cerevisiae GN = URA6 PE = 1 UMPK_YEAST 22,933.90 12 0 SV =1 Myosin light chain 1 OS = Saccharomyces cerevisiae GN = MLC1 PE = 1MLC1_YEAST 16,445.30 24 1 SV = 1 Glucose-repressible alcoholdehydrogenase transcriptional effector CCR4_YEAST 94,702.70 12 0 OS =Saccharomyces cerevisiae GN = CCR4 PE = 1 SV = 1 54S ribosomal proteinL1, mitochondrial OS = Saccharomyces RM01_YEAST 30,997.30 12 0cerevisiae GN = MRPL1 PE = 1 SV = 1 Nuclear polyadenylated RNA-bindingprotein 3 OS = Saccharomyces NAB3_YEAST 90,438.50 12 0 cerevisiae GN =NAB3 PE = 1 SV = 1 Phosphoglycerate mutase 2 OS = Saccharomycescerevisiae PMG2_YEAST 36,074.50 12 0 GN = GPM2 PE = 1 SV = 13.(45.-bisphosphate nucleotidase OS = Saccharomyces cerevisiaeHAL2_YEAST 39,150.30 12 0 GN = HAL2 PE = 1 SV = 1 Protein SEY1 OS =Saccharomyces cerevisiae (strain AW RI1631) SEY1_YEAS6 89,425.20 12 0 GN= SEY1 PE = 3 SV = 1 (+2) Thiamine metabolism regulatory protein THI3 OS= Saccharomyces THI3_YEAST 68,367.90 12 0 cerevisiae GN = THI3 PE = 1 SV= 1 Alpha-mannosidase OS = Saccharomyces cerevisiae GN = AMS1 PE = 1MAN1_YEAST 124,503.20 24 1 SV = 2 [NU+] prion formation protein 1 OS =Saccharomyces cerevisiae NEW1_YEAST 134,335.50 12 0 GN = NEW1 PE = 1 SV= 1 T-complex protein 1 subunit beta OS = Saccharomyces cerevisiaeTCPB_YEAST 57,205.70 12 0 GN = CCT2 PE = 1 SV = 1 Putative zincmetalloproteinase YIL108W OS = Saccharomyces YIK8_YEAST 77,416.50 12 0cerevisiae GN = YIL108W PE = 1 SV = 1 Prefoldin subunit 5 OS =Saccharomyces cerevisiae GN = GIM5 PE = 1 PFD5_YEAST 18,356.30 12 0 SV =1 Probable glycosidase CRH2 OS = Saccharomyces cerevisiae CRH2_YEAST49,906.20 12 0 GN = UTR2 PE = 1 SV = 3 Coatomer subunit epsilon OS =Saccharomyces cerevisiae GN = SEC28 COPE_YEAST 33,830.60 12 0 PE = 1 SV= 2 26S proteasome regulatory subunit RPN13 OS = SaccharomycesRPN13_YEAST 17,902.50 12 0 cerevisiae GN = RPN13 PE = 1 SV = 1 40Sribosomal protein S28-A OS = Saccharomyces cerevisiae RS28A_YEAST7,591.70 24 1 GN = RPS28A PE = 1 SV = 1 D-3-phosphoglyceratedehydrogenase 1 OS = Saccharomyces SERA_YEAST 51,194.10 12 0 cerevisiaeGN = SER3 PE = 1 SV = 1 Adenylosuccinate synthetase OS = Saccharomycescerevisiae AURA_YEAST 48,280.40 12 0 GN = ADE12 PE = 1 SV = 3 CTPsynthase 2 OS = Saccharomyces cerevisiae (strain YJM789) URA8_YEAS764,497.40 12 0 GN = URA8 PE = 3 SV = 1 (+1) ATP-dependent RNA helicaseHAS1 OS = Saccharomyces cerevisiae HAS1_YEAST 56,720.20 12 0 GN = HAS1PE = 1 SV = 1 Zinc finger protein ZPR1 OS = Saccharomyces cerevisiae GN= ZPR1 ZPR1_YEAST 55,072.70 12 0 PE = 1 SV = 1 26S proteasome regulatorysubunit RPN3 OS = Saccharomyces RPN3_YEAST 60,426.30 12 0 cerevisiae GN= RPN3 PE = 1 SV = 4 Peroxisomal membrane protein PMP27 OS =Saccharomyces PEX11_YEAST 26,876.20 12 0 cerevisiae GN = PEX11 PE = 1 SV= 2 Ribose-phosphate pyrophosphokinase 5 OS = Saccharomyces KPR5_YEAST53,506.20 12 0 cerevisiae GN = PRS5 PE = 1 SV = 1 U6 snRNA-associatedSm-like protein LSm6 OS = Saccharomyces LSM6_YEAS7 9,398.00 12 0cerevisiae (strain YJM789) GN = LSM6 PE = 3 SV = 1 (+1) Protein HMF1 OS= Saccharomyces cerevisiae GN = HMF1 PE = 1 SV = 1 HMF1_YEAST 13,905.9012 0 General negative regulator of transcription subunit 1 NOT1_YEAST240,344.80 12 0 OS = Saccharomyces cerevisiae GN = NOT1 PE = 1 SV = 2Putative glucokinase-2 OS = Saccharomyces cerevisiae GN = EMI2EMI2_YEAST 55,923.00 92 4 PE = 1 SV = 1 26S protease regulatory subunit4 homolog OS = Saccharomyces PRS4_YEAST 48,830.50 23 1 cerevisiae GN =RPT2 PE = 1 SV = 3 Sphingolipid long chain base-responsive protein LSP1LSP1_YEAST 38,071.60 113 5 OS = Saccharomyces cerevisiae GN = LSP1 PE =1 SV = 1 UPF0001 protein YBL036C OS = Saccharomyces cerevisiaeYBD6_YEAST 29,124.20 11 0 GN = YBL036C PE = 1 SV = 1 Galactose/lactosemetabolism regulatory protein GAL80 GAL80_YEAST 48,325.40 11 0 OS =Saccharomyces cerevisiae GN = GAL80 PE = 1 SV = 2 U3 small nucleolarribonucleoprotein protein IMP3 IMP3_YEAST 21,886.10 11 0 OS =Saccharomyces cerevisiae GN = IMP3 PE = 1 SV = 1 U3 small nucleolarRNA-associated protein 21 OS = Saccharomyces UTP21_YEAST 104,794.60 11 0cerevisiae GN = UTP21 PE = 1 SV = 1 DNA polymerase alpha catalyticsubunit A OS = Saccharomyces DPOA_YEAST 166,815.30 11 0 cerevisiae GN =POL1 PE = 1 SV = 2 Probable glycerophosphodiester phosphodiesteraseYPL206C YP206_YEAST 37,071.30 11 0 OS = Saccharomyces cerevisiae GN =YPL206C PE = 1 SV = 1 Cytochrome c oxidase assembly protein COX15 OS =Saccharomyces COX15_YEAST 54,660.50 11 0 cerevisiae GN = COX15 PE = 1 SV= 1 U6 snRNA-associated Sm-like protein LSm5 OS = SaccharomycesLSM5_YEAST 10,423.20 11 0 cerevisiae GN = LSM5 PE = 1 SV = 1 60Sribosomal protein L29 OS = Saccharomyces cerevisiae GN = RPL29RL29_YEAST 6,669.10 11 0 PE = 1 SV = 3 Tricalbin-3 OS = Saccharomycescerevisiae GN = TCB3 PE = 1 SV = 1 TCB3_YEAST 171,081.40 22 1Peroxiredoxin HYR1 OS = Saccharomyces cerevisiae GN = HYR1 PE = 1GPX3_YEAST 18,642.20 22 1 SV = 1 Glucose-6-phosphate 1-dehydrogenase OS= Saccharomyces G6PD_YEAST 57,523.60 44 2 cerevisiae GN = ZWF1 PE = 1 SV= 4 Endosomal protein P24B OS = Saccharomyces cerevisiae GN = EMP24EMP24_YEAST 23,332.70 11 0 PE = 1 SV = 1 Proteasome component Cl OS =Saccharomyces cerevisiae PSA3_YEAST 31,536.40 11 0 GN = PRE10 PE = 1 SV= 2 26S proteasome regulatory subunit RPN6 OS = Saccharomyces RPN6_YEAST49,776.20 11 0 cerevisiae GN = RPN6 PE = 1 SV = 3 Monothiolglutaredoxin-3 OS = Saccharomyces cerevisiae GN = GRX3 GLRX3_YEAST32,481.70 11 0 PE = 1 SV = 1 C-8 sterol isomerase OS = Saccharomycescerevisiae GN = ERG2 PE = 1 ERG2_YEAST 24,896.60 11 0 SV = 1Uncharacterized membrane glycoprotein YNR065C YN94_YEAST 125,204.80 11 0OS = Saccharomyces cerevisiae GN = YNR065C PE = 1 SV = 1 Ubiquitincarboxyl-terminal hydrolase 6 OS = Saccharomyces UBP6_YEAST 57,112.50 110 cerevisiae GN = UBP6 PE = 1 SV = 1 Histone chaperone ASF1 OS =Saccharomyces cerevisiae GN = ASF1 ASF1_YEAST 31,603.10 11 0 PE = 1 SV =1 Pumilio homology domain family member 6 OS = Saccharomyces PUF6_YEAST75,109.00 22 1 cerevisiae GN = PUF6 PE = 1 SV = 1 Mitochondrial outermembrane protein OM14 OS = Saccharomyces OM14_YEAS7 14,609.90 11 0cerevisiae (strain YJM789) GN = OM14 PE = 3 SV = 1 (+1) AP-1 complexsubunit gamma-1 OS = Saccharomyces cerevisiae AP1G1_YEAST 93,631.50 11 0GN = APL4 PE = 1 SV = 1 Signal recognition particle subunit SRP72 OS =Saccharomyces SRP72_YEAST 73,544.80 11 0 cerevisiae GN = SRP72 PE = 1 SV= 2 Protein transport protein SEC31 OS = Saccharomyces cerevisiaeSEC31_YEAST 138,706.80 11 0 GN = SEC31 PE = 1 SV = 2Phosphatidylethanolamine N-methyltransferase OS = SaccharomycesPEM1_YEAST 101,208.50 11 0 cerevisiae GN = PEM1 PE = 1 SV = 1Mitochondrial import inner membrane translocase subunit TIM16TIM16_YEAST 16,216.50 11 0 OS = Saccharomyces cerevisiae GN = PAM16 PE =1 SV = 1 Phosphatidate cytidylyltransferase OS = Saccharomycescerevisiae CDS1_YEAST 51,825.70 11 0 GN = CDS1 PE = 1 SV = 1 26Sproteasome regulatory subunit RPN12 OS = Saccharomyces RPN12_YEAST31,922.00 11 0 cerevisiae GN = RPN12 PE = 1 SV = 3 N-terminalacetyltransferase A complex subunit NAT1 NAT1_YEAST 98,912.00 11 0 OS =Saccharomyces cerevisiae GN = NAT1 PE = 1 SV = 2 Nucleolarpre-ribosomal-associated protein 1 OS = Saccharomyces URB1_YEAST203,299.10 11 0 cerevisiae GN = URB1 PE = 1 SV = 2 GU4 nucleic-bindingprotein 1 OS = Saccharomyces cerevisiae G4P1_YEAST 42,084.50 87 4 GN =ARC1 PE = 1 SV = 2 Mitochondrial peculiar membrane protein 1 OS =Saccharomyces MPM1_YEAST 28,471.40 43 2 cerevisiae GN = MPM1 PE = 1 SV =1 6-phosphogluconate dehydrogenase, decarboxylating 1 6PGD1_YEAST53,545.30 494 23 OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1Transcription-associated protein 1 OS = Saccharomyces cerevisiaeTRA1_YEAST 433,195.70 21 1 GN = TRA1 PE = 1 SV = 1 RNApolymerase-associated protein CTR9 OS = Saccharomyces CTR9_YEAST124,663.10 42 2 cerevisiae GN = CTR9 PE = 1 SV = 2 DNA-directed RNApolymerases I, II, and III subunit RPABC3 RPAB3_YEAST 16,512.10 21 1 OS= Saccharomyces cerevisiae GN = RPB8 PE = 1 SV = 1Ribonucleoside-diphosphate reductase large chain 1 RIR1_YEAST 99,564.5021 1 OS = Saccharomyces cerevisiae GN = RNR1 PE = 1 SV = 2 60S ribosomalprotein L10 OS = Saccharomyces cerevisiae GN = RPL10 RL10_YEAST25,362.10 168 8 PE = 1 SV = 1 Sphingolipid long chain base-responsiveprotein PIL1 PIL1_YEAST 38,350.30 166 8 OS = Saccharomyces cerevisiae GN= PIL1 PE = 1 SV = 1 Ribosome-associated complex subunit SSZ1 OS =Saccharomyces SSZ1 _YEAST 58,239.50 145 7 cerevisiae GN = SSZ1 PE = 1 SV= 2 Golgin IMH1 OS = Saccharomyces cerevisiae GN = IMH1 PE = 1 SV = 1IMH1_YEAST 105,231.40 10 0 Protein SCO2, mitochondrial OS =Saccharomyces cerevisiae SCO2_YEAST 34,890.60 10 0 GN = SCO2 PE = 1 SV =1 3-ketoacyl-CoA reductase OS = Saccharomyces cerevisiae GN = IFA38MKAR_YEAST 38,709.70 10 0 PE = 1 SV = 1 Iron transport multicopperoxidase FET5 OS = Saccharomyces FET5_YEAST 70,880.90 10 0 cerevisiae GN= FET5 PE = 1 SV = 1 Protein ISD11 OS = Saccharomyces cerevisiae GN =ISD11 PE = 1 SV = 1 ISD11_YEAST 11,266.40 10 0 Mitochondrialdistribution and morphology protein 38 MDM38_YEAST 65,008.10 10 0 OS =Saccharomyces cerevisiae GN = MDM38 PE = 1 SV = 1 Elongation of fattyacids protein 3 OS = Saccharomyces cerevisiae ELO3_YEAST 39,467.00 10 0GN = ELO3 PE = 1 SV = 1 Nucleolar GTP-binding protein 1 OS =Saccharomyces cerevisiae NOG1_YEAST 74,412.80 10 0 GN = NOG1 PE = 1 SV =1 Peptidyl-prolyl cis-trans isomerase ESS1 OS = Saccharomyces ESS1_YEAST19,404.90 10 0 cerevisiae GN = ESS1 PE = 1 SV = 3 ATPase GET3 OS =Saccharomyces cerevisiae (strain RM11-1a) GET3_YEAS1 39,355.10 10 0 GN =GET3 PE = 3 SV = 1 (+2) Protein APA1 OS = Saccharomyces cerevisiae GN =APA1 PE = 1 SV = 4 APA1_YEAST 36,494.20 10 0 Mitochondrial respiratorychain complexes assembly protein AFG3 AFG3_YEAST 84,547.40 10 0 OS =Saccharomyces cerevisiae GN = AFG3 PE = 1 SV = 1 Calcium-transportingATPase 2 OS = Saccharomyces cerevisiae ATC2_YEAST 130,866.40 10 0 GN =PMC1 PE = 1 SV = 1 Probable intramembrane protease YKL1000 OS =Saccharomyces YKK0_YEAST 67,528.20 10 0 cerevisiae GN = YKL1000 PE = 1SV = 1 KH domain-containing protein YBL032W OS = SaccharomycesYBD2_YEAST 41,684.60 10 0 cerevisiae GN = YBL032W PE = 1 SV = 1Mitochondrial import receptor subunit TOM22 OS = SaccharomycesTOM22_YEAST 16,790.90 10 0 cerevisiae GN = TOM22 PE = 1 SV = 3 ProteinMSP1 OS = Saccharomyces cerevisiae GN = MSP1 PE = 1 SV = 2 MSP1_YEAST40,346.50 10 0 UPF0364 protein YMR027W OS = Saccharomyces cerevisiaeYMR7_YEAST 54,130.90 10 0 GN = YMR027W PE = 1 SV = 1 Uncharacterizedprotein YJL217W OS = Saccharomyces cerevisiae YJV7_YEAST 21,966.80 10 0GN = YJL217W PE = 1 SV = 1 ER membrane protein complex subunit 4 OS =Saccharomyces EMC4_YEAST 21,460.70 10 0 cerevisiae GN = EMC4 PE = 1 SV =1 Sm-like protein LSmi OS = Saccharomyces cerevisiae GN = LSM1LSM1_YEAST 20,307.60 10 0 PE = 1 SV = 1 Probablealpha-1,6-mannosyltransferase MNN10 OS = Saccharomyces MNN10_YEAST46,750.50 10 0 cerevisiae GN = MNN10 PE = 1 SV = 1 Protein HAM1 OS =Saccharomyces cerevisiae GN = HAM1 PE = 1 SV = 1 HAM1_YEAST 22,093.90 100 NADPH-dependent methylglyoxal reductase GRE2 GRE2_YEAST 38,170.30 10 0OS = Saccharomyces cerevisiae GN = GRE2 PE = 1 SV = 1 Alpha-1,2mannosyltransferase KTR1 OS = Saccharomyces cerevisiae KTR1_YEAST46,023.70 10 0 GN = KTR1 PE = 1 SV = 1 Protein VTH1 OS = Saccharomycescerevisiae GN = VTH1 PE = 1 SV = 1 VTH1_YEAST 174,434.90 10 0 (+1)Trehalose synthase complex regulatory subunit TPS3 TPS3_YEAST 118,837.5010 0 OS = Saccharomyces cerevisiae GN = TPS3 PE = 1 SV = 3 Heat shockprotein 60, mitochondrial OS = Saccharomyces cerevisiae HSP60_YEAST60,753.00 743 38 GN = HSP60 PE = 1 SV = 1 Pyruvate dehydrogenase E1component subunit beta, mitochondrial ODPB_YEAST 40,054.20 77 4 OS =Saccharomyces cerevisiae GN = PDB1 PE = 1 SV = 2 Pyruvate dehydrogenaseE1 component subunit alpha, mitochondrial ODPA_YEAST 46,344.40 96 5 OS =Saccharomyces cerevisiae GN = PDA1 PE = 1 SV = 2 Actin-related protein 3OS = Saccharomyces cerevisiae GN = ARP3 ARP3_YEAST 49,542.70 19 1 PE = 1SV = 1 AMP deaminase OS = Saccharomyces cerevisiae GN = AMD1 PE = 1AMPD_YEAST 93,304.30 19 1 SV = 2 Lon protease homolog, mitochondrial OS= Saccharomyces cerevisiae LONM_YEAST 127,116.80 56 3 GN = PIM1 PE = 1SV = 2 Isocitrate dehydrogenase [NAD] subunit 1, mitochondrialIDH1_YEAST 39,325.30 223 12 OS = Saccharomyces cerevisiae GN = IDH1 PE =1 SV = 2 Serine hydroxymethyltransferase, cytosolic OS = SaccharomycesGLYC_YEAST 52,219.70 110 6 cerevisiae GN = SHM2 PE = 1 SV = 2 Rabproteins geranylgeranyltransferase component A RAEP_YEAST 67,374.90 9 0OS = Saccharomyces cerevisiae GN = MRS6 PE = 1 SV = 2 37S ribosomalprotein MRP1, mitochondrial OS = Saccharomyces RT01_YEAST 36,730.90 9 0cerevisiae GN = MRP1 PE = 1 SV = 2 Carboxypeptidase S OS = Saccharomycescerevisiae GN = CPS1 PE = 1 CBPS_YEAST 64,599.30 9 0 SV = 2 Probableglucose transporter HXT5 OS = Saccharomyces cerevisiae HXT5_YEAST66,252.90 9 0 GN = HXT5 PE = 1 SV = 1 Glycerol-3-phosphatedehydrogenase, mitochondrial GPDM_YEAST 72,390.60 90 5 OS =Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2 Cytochrome b2,mitochondrial OS = Saccharomyces cerevisiae CYB2_YEAST 65,541.20 9 0 GN= CYB2 PE = 1 SV = 1 Translation machinery-associated protein 20 OS =Saccharomyces TMA20_YEAST 20,278.30 9 0 cerevisiae GN = TMA20 PE = 1 SV= 1 D-arabinono-1,4-lactone oxidase OS = Saccharomyces cerevisiaeALO_YEAST 59,494.80 9 0 GN = ALO1 PE = 1 SV = 1 Protein phosphatase 2Chomolog 3 OS = Saccharomyces cerevisiae PP2C3_YEAST 51,391.60 9 0 GN =PTC3 PE = 1 SV = 3 DNA-directed RNA polymerase II subunit RPB9 OS =Saccharomyces RPB9_YEAST 14,288.00 9 0 cerevisiae GN = RPB9 PE = 1 SV =1 Casein kinase II subunit alpha OS = Saccharomyces cerevisiaeCSK21_YEAST 44,669.80 9 0 GN = CKA1 PE = 1 SV = 1 26S proteaseregulatory subunit 6A OS = Saccharomyces cerevisiae PRS6A_YEAST48,257.20 9 0 GN = RPT5 PE = 1 SV = 3 Enoyl reductase TSC13 OS =Saccharomyces cerevisiae GN = TSC13 TSC13_YEAST 36,770.00 9 0 PE = 1 SV= 1 H/ACA ribonucleoprotein complex subunit 2 OS = SaccharomycesNHP2_YEAST 17,122.10 9 0 cerevisiae GN = NHP2 PE = 1 SV = 2 Retrograderegulation protein 2 OS = Saccharomyces cerevisiae RTG2_YEAST 65,573.609 0 GN = RTG2 PE = 1 SV = 2 Uncharacterized protein YDR476C OS =Saccharomyces cerevisiae YD476_YEAST 25,266.70 9 0 GN = YDR476C PE = 1SV = 1 DNA-directed RNA polymerases I and III subunit RPAC2 RPAC2_YEAST16,150.90 9 0 OS = Saccharomyces cerevisiae GN = RPC19 PE = 1 SV = 1 GPItransamidase component GPI16 OS = Saccharomyces cerevisiae GPI16_YEAST68,775.10 9 0 GN = GPI16 PE = 1 SV = 2 V-type proton ATPase subunit e OS= Saccharomyces cerevisiae VA0E_YEAST 8,381.10 9 0 GN = VMA9 PE = 1 SV =1 Cell division control protein 28 OS = Saccharomyces cerevisiaeCDC28_YEAST 34,063.40 18 1 GN = CDC28 PE = 1 SV = 1Serine/threonine-protein phosphatase 2B catalytic subunit A2 PP2B2_YEAST68,529.90 9 0 OS = Saccharomyces cerevisiae GN = CNA2 PE = 1 SV = 2GTP-binding protein YPT31/YPT8 OS = Saccharomyces cerevisiae YPT31_YEAST24,469.90 9 0 GN = YPT31 PE = 1 SV = 3 (+1) FK506-binding nuclearprotein OS = Saccharomyces cerevisiae FKBP3_YEAST 46,554.20 9 0 GN =FPR3 PE = 1 SV = 2 D-3-phosphoglycerate dehydrogenase 2 OS =Saccharomyces SER33_YEAST 51,189.50 9 0 cerevisiae GN = SER33 PE = 1 SV= 1 Coatomer subunit beta OS = Saccharomyces cerevisiae GN = SEC26COPB_YEAST 109,023.60 9 0 PE = 1 SV = 2 Dipeptidyl aminopeptidase B OS =Saccharomyces cerevisiae DAP2_YEAST 93,406.70 9 0 GN = DAP2 PE = 2 SV =2 Protein UTH1 OS = Saccharomyces cerevisiae (strain RM11-1a) UTH1_YEAS136,735.90 9 0 GN = UTH1 PE = 3 SV = 1 (+3) Uncharacterizedoxidoreductase YML125C OS = Saccharomyces YMM5_YEAST 35,288.60 9 0cerevisiae GN = YML125C PE = 1 SV = 1 Long-chain-fatty-acid--CoA ligase3 OS = Saccharomyces cerevisiae LCF3_YEAST 77,948.60 9 0 GN = FAA3 PE =1 SV = 1 Actin-related protein 2/3 complex subunit 2 OS = SaccharomycesARPC2_YEAST 39,567.70 18 1 cerevisiae GN = ARC35 PE = 1 SV = 1 Ceramidevery long chain fatty acid hydroxylase SCS7 SCS7_YEAST 44,882.80 9 0 OS= Saccharomyces cerevisiae GN = SCS7 PE = 1 SV = 1 Protein SDS24 OS =Saccharomyces cerevisiae (strain YJM789) SDS24_YEAS7 57,188.20 9 0 GN =SDS24 PE = 3 SV = 1 (+1) Cytochrome c oxidase assembly protein COX14 OS= Saccharomyces COX14_YEAST 7,959.10 9 0 cerevisiae GN = COX14 PE = 1 SV= 1 Signal recognition particle subunit SRP14 OS = SaccharomycesSRP14_YEAST 16,430.30 9 0 cerevisiae GN = SRP14 PE = 1 SV = 1 Putativeguanine nucleotide-exchange factor SED4 SED4_YEAST 114,081.60 9 0 OS =Saccharomyces cerevisiae GN = SED4 PE = 1 SV = 1 Cytochrome b-c1 complexsubunit 1, mitochondrial QCR1_YEAST 50,229.00 71 4 OS = Saccharomycescerevisiae GN = COR1 PE = 1 SV = 1 Lysyl-tRNA synthetase, cytoplasmic OS= Saccharomyces cerevisiae SYKC_YEAST 67,960.50 88 5 GN = KRS1 PE = 1 SV= 2 Glutamyl-tRNA synthetase, cytoplasmic OS = Saccharomyces SYEC_YEAST80,846.20 246 14 cerevisiae GN = GUS1 PE = 1 SV = 3 Protein transportprotein SEC13 OS = Saccharomyces cerevisiae SEC13_YEAST 33,042.60 35 2GN = SEC13 PE = 1 SV = 1 Threonyl-tRNA synthetase, cytoplasmic OS =Saccharomyces SYTC_YEAST 84,522.60 121 7 cerevisiae GN = THS1 PE = 1 SV= 2 Uncharacterized protein YMR178W OS = Saccharomyces cerevisiaeYM44_YEAST 31,145.60 51 3 GN = YMR178W PE = 1 SV = 1 40S ribosomalprotein S25-A OS = Saccharomyces cerevisiae RS25A_YEAST 12,039.90 68 4GN = RPS25A PE = 1 SV = 1 (+1) Transposon Ty2-LR1 Gag-Pol polyprotein OS= Saccharomyces YL21B_YEAST 202,130.30 17 1 cerevisiae GN = TY2B-LR1 PE= 3 SV = 1 Farnesyl pyrophosphate synthase OS = Saccharomyces cerevisiaeFPPS_YEAST 40,485.30 135 8 GN = FPP1 PE = 1 SV = 2 Isocitratedehydrogenase [NAD] subunit 2, mitochondrial IDH2_YEAST 39,740.60 151 9OS = Saccharomyces cerevisiae GN = IDH2 PE = 1 SV = 1 Nascentpolypeptide-associated complex subunit beta-1 NACB1_YEAS7 17,020.50 33 2OS = Saccharomyces cerevisiae (strain YJM789) GN = EGD1 PE = 3 (+1) SV =1 40S ribosomal protein S3 OS = Saccharomyces cerevisiae GN = RPS3RS3_YEAST 26,503.00 296 18 PE = 1 SV = 5 ATP-dependent RNA helicase SUB2OS = Saccharomyces cerevisiae SUB2_YEAS7 50,280.10 49 3 (strain YJM789)GN = SUB2 PE = 3 SV = 1 (+1) Elongation factor 1-gamma 2 OS =Saccharomyces cerevisiae EF1G2_YEAST 46,521.90 98 6 GN = TEF4 PE = 1 SV= 1 Fold NSAF NSAF enriched Protein TAL-PrA Wild type TAL-PrA/WT RankRank/N Plasma membrane ATPase 1 OS = Saccharomyces 0.003000442.19206E-05 136.8778684 1 0.001956947 cerevisiae GN = PMA1 PE = 1 SV = 2Transposon Ty1-H Gag-Pol polyprotein 0.000721016 1.07667E-05 66.967129162 0.003913894 OS = Saccharomyces cerevisiae GN = TY1B-H PE = 1 SV = 1ATP-dependent RNA helicase DED1 0.002132761 3.33122E-05 64.02351908 30.005870841 OS = Saccharomyces cerevisiae (strain YJM789) GN = DED1 PE =3 SV = 1 Protein TIF31 OS = Saccharomyces cerevisiae 0.0008339361.50427E-05 55.43798971 4 0.007827789 GN = TIF31 PE = 1 SV = 1 ProteinURA1 OS = Saccharomyces cerevisiae 0.002963245 5.34515E-05 55.43798971 50.009784736 GN = URA2 PE = 1 SV = 4 Elongation factor 3B OS =Saccharomyces cerevisiae 0.001017068 1.88464E-05 53.96618467 60.011741683 GN = HEF3 PE = 1 SV = 2 Transposon Ty1-OL Gag polyprotein0.002361064 4.4561 E-05 52.98498131 7 0.01369863 OS = Saccharomycescerevisiae GN = TY1A-OL PE = 1 SV = 1 40S ribosomal protein S1 -B OS =Saccharomyces 0.003792691 7.57911E-05 50.04137124 8 0.015655577cerevisiae (strain RM11-1a) GN = RPS1 B PE = 3 SV = 1 40S ribosomalprotein S1 -A OS = Saccharomyces 0.003522263 7.59733E-05 46.36185865 90.017612524 cerevisiae (strain RM11-1a) GN = RPS1A PE = 3 SV = 1Transposon Ty1-DR3 Gag polyprotein 0.002047426 4.43968E-05 46.1165578110 0.019569472 OS = Saccharomyces cerevisiae GN = TY1A-DR3 PE = 1 SV = 1Galactose transporter OS = Saccharomyces cerevisiae 0.0015406853.43213E-05 44.89005361 11 0.021526419 GN = GAL2 PE = 1 SV = 3Argininosuccinate synthase OS = Saccharomyces 0.002019878 4.65214E-0543.41824857 12 0.023483366 cerevisiae GN = ARG1 PE = 1 SV = 2Pleiotropic ABC efflux transporter of multiple drugs 0.0004777121.28122E-05 37.28572759 13 0.025440313 OS = Saccharomyces cerevisiae GN= PDR5 PE = 1 SV = 1 1,3-beta-glucan synthase component FKS1 0.0003764671.01637E-05 37.04042675 14 0.02739726 OS = Saccharomyces cerevisiae GN =FKS1 PE = 1 SV = 2 Heat shock protein SSC3, mitochondrial 0.0011464593.11579E-05 36.79512591 15 0.029354207 OS = Saccharomyces cerevisiae GN= ECM10 PE = 1 SV = 1 Pyruvate decarboxylase isozyme 3 OS =Saccharomyces 0.001304785 3.54608E-05 36.79512591 16 0.031311155cerevisiae GN = PDC6 PE = 1 SV = 3 Nuclear segregation protein BFR1 OS =Saccharomyces 0.001343076 3.99651E-05 33.606215 17 0.033268102cerevisiae GN = BFR1 PE = 1 SV = 1 60S ribosomal protein L18 OS =Saccharomyces 0.003360413 0.000106195 31.64380828 18 0.035225049cerevisiae GN = RP L18A PE = 1 SV = 1 40S ribosomal protein S2 OS =Saccharomyces 0.002458834 7.95536E-05 30.90790577 19 0.037181996cerevisiae GN = RPS2 PE = 1 SV = 3 1,3-beta-glucan synthase componentGSC2 0.000311042 1.00635E-05 30.90790577 20 0.039138943 OS =Saccharomyces cerevisiae GN = GSC2 PE = 1 SV = 2 6-phosphogluconatedehydrogenase, decarboxylating 2 0.001172178 4.0496E-05 28.94549905 210.04109589 OS = Saccharomyces cerevisiae GN = GND2 PE = 1 SV = 1High-affinity hexose transporter HXT6 0.00092217 3.48087E-05 26.4924906622 0.043052838 OS = Saccharomyces cerevisiae GN = HXT7 PE = 1 SV = 1Protein GAL3 OS = Saccharomyces cerevisiae GN = GAL3 0.0009860183.75666E-05 26.24718982 23 0.045009785 PE = 1 SV = 2 ATP-dependent RNAhelicase MSS116, mitochondrial 0.000737438 2.8631 E-05 25.75658814 240.046966732 OS = Saccharomyces cerevisiae GN = MSS116 PE = 1 SV = 1Probable cation transporting ATPase 1 0.000388073 1.61431 E-0524.03948226 25 0.048923679 OS = Saccharomyces cerevisiae GN = SPF1 PE =1 SV = 1 High-affinity hexose transporter HXT6 0.000837185 3.48254E-0524.03948226 26 0.050880626 OS = Saccharomyces cerevisiae GN = HXT6 PE =1 SV = 2 Eukaryotic translation initiation factor 5B 0.0004675851.94507E-05 24.03948226 26 0.050880626 OS = Saccharomyces cerevisiae GN= FUN12 PE = 1 SV = 2 DNA-directed RNA polymerase II subunit RPB10.000268377 1.13966E-05 23.54888058 28 0.054794521 OS = Saccharomycescerevisiae GN = RPB1 PE = 1 SV = 2 1,3-beta-glucanosyltransferase GAS10.0008451 3.66506E-05 23.0582789 29 0.056751468 OS = Saccharomycescerevisiae GN = GAS1 PE = 1 SV = 2 Eukaryotic translation initiationfactor 3 subunit B 0.00056527 2.47784E-05 22.81297806 30 0.058708415 OS= Saccharomyces cerevisiae (strain YJM789) GN = PRT1 PE = 3 SV = 1Phosphoglucomutase-1 OS = Saccharomyces cerevisiae 0.0007723523.45999E-05 22.32237639 31 0.060665362 GN = PGM1 PE = 1 SV = 1 T-complexprotein 1 subunit gamma 0.000819711 3.71295E-05 22.07707555 320.062622309 OS = Saccharomyces cerevisiae GN = CCT3 PE = 1 SV = 2 FACTcomplex subunit SPT16 OS = Saccharomyces 0.000397347 1.84072E-0521.58647387 33 0.064579256 cerevisiae GN = SPT16 PE = 1 SV = 1ATP-dependent RNA helicase DBP1 0.000685433 3.21179E-05 21.34117303 340.066536204 OS = Saccharomyces cerevisiae (strain YJM789) GN = DBP1 PE =3 SV = 1 Dihydrolipoyllysine-residue acetyltransferase component0.00089935 4.21415E-05 21.34117303 34 0.066536204 of pyruvatedehydrogenase complex, mitochondrial OS = Saccharomyces cerevisiae GN =PDA2 PE = 1 SV = 1 Clathrin heavy chain OS = Saccharomyces cerevisiae0.000494931 2.33254E-05 21.21852261 36 0.070450098 GN = CHC1 PE = 1 SV =1 40S ribosomal protein S8 OS = Saccharomyces 0.002048356 9.70975E-0521.09587219 37 0.072407045 cerevisiae GN = RPS8A PE = 1 SV = 3DNA-directed RNA polymerase II subunit RPB2 0.000328146 1.5738E-0520.85057135 38 0.074363992 OS = Saccharomyces cerevisiae GN = RPB2 PE =1 SV = 2 Glutamine synthetase OS = Saccharomyces cerevisiae 0.001026035.22842E-05 19.62406715 39 0.076320939 GN = GLN1 PE = 1 SV = 2Mitochondrial import receptor subunit TOM40 0.001006641 5.19456E-0519.37876631 40 0.078277886 OS = Saccharomyces cerevisiae GN = TOM40 PE =1 SV = 1 C-1-tetrahydrofolate synthase, cytoplasmic 0.0003983232.1366E-05 18.64286379 41 0.080234834 OS = Saccharomyces cerevisiae GN =ADE3 PE = 1 SV = 1 rRNA 2′-O-methyltransferase fibrillarin 0.0011656846.33608E-05 18.39756296 42 0.082191781 OS = Saccharomyces cerevisiae GN= NOP1 PE = 1 SV = 1 Protein SCP160 OS = Saccharomyces cerevisiae0.001192042 6.47935E-05 18.39756296 42 0.082191781 GN = SCP160 PE = 1 SV= 3 Protein transport protein SEC23 OS = Saccharomyces 0.0004579652.55747E-05 17.90696128 44 0.086105675 cerevisiae GN = SEC23 PE = 1 SV =1 Nucleolar protein 56 OS = Saccharomyces cerevisiae 0.000687645 3.8401E-05 17.90696128 45 0.088062622 GN = NOP56 PE = 1 SV = 1 Orotidine 5′phosphate decarboxylase 0.001300706 7.4683E-05 17.4163596 46 0.090019569OS = Saccharomyces cerevisiae GN = URA3 PE = 1 SV = 2 Homocitratesynthase, cytosolic isozyme 0.000773374 4.63641 E-05 16.68045708 470.091976517 OS = Saccharomyces cerevisiae GN = LYS20 PE = 1 SV = 1External NADH-ubiquinone oxidoreductase 1, 0.000571718 3.47863E-0516.43515624 48 0.093933464 mitochondrial OS = Saccharomyces cerevisiaeGN = NDE1 PE = 1 SV = 1 Eukaryotic translation initiation factor 3subunit C 0.000384987 2.34246E-05 16.43515624 49 0.095890411 OS =Saccharomyces cerevisiae (strain YJM789) GN = NIP1 PE = 3 SV = 1 ZuotinOS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 0.00072121 4.4547E-0516.1898554 50 0.097847358 SV = 1 Trehalose phosphataseOS = Saccharomycescerevisiae 0.000327715 2.12059E-05 15.45395288 51 0.099804305 GN = TPS2PE = 1 SV = 3 Saccharopepsin OS = Saccharomyces cerevisiae 0.0007583594.90722E-05 15.45395288 51 0.099804305 GN = PEP4 PE = 1 SV = 1 rRNAbiogenesis protein RRP5 OS = Saccharomyces 0.000174731 1.13065E-0515.45395288 53 0.1037182 cerevisiae GN = RRP5 PE = 1 SV = 1cAMP-dependent protein kinase regulatory subunit 0.000703343 4.62462E-0515.20865204 54 0.105675147 OS = Saccharomyces cerevisiae GN = BCY1 PE =1 SV = 4 Galactokinase OS = Saccharomyces cerevisiae 0.0124802130.000829109 15.05255151 55 0.107632094 GN = GAL1 PE = 1 SV = 4 Probable2-methylcitrate dehydratase 0.000566456 3.78562E-05 14.9633512 560.109589041 OS = Saccharomyces cerevisiae GN = PDH1 PE = 1 SV = 12-isopropylmalate synthase 2, mitochondrial 0.000486249 3.2496E-0514.9633512 57 0.111545988 OS = Saccharomyces cerevisiae GN = LEU9 PE = 1SV = 1 NADH-cytochrome b5 reductase 2 OS = Saccharomyces 0.0009579966.40228E-05 14.9633512 58 0.113502935 cerevisiae (strain YJM789) GN =MCR1 PE = 2 SV = 1 6,7-dimethyl-8-ribityllumazine synthase 0.0017321210.000117687 14.71805036 59 0.115459883 OS = Saccharomyces cerevisiae GN= RIB4 PE = 1 SV = 2 N-(5′-phosphoribosyl)anthranilate isomerase0.001331159 9.0444E-05 14.71805036 59 0.115459883 OS = Saccharomycescerevisiae GN = TRP1 PE = 1 SV = 2 Glutamate synthase [NADH] OS =Saccharomyces 0.000130484 9.17129E-06 14.22744869 61 0.119373777cerevisiae GN = GLT1 PE = 1 SV = 2 Nuclear localization sequence-bindingprotein 0.000661538 4.90335E-05 13.49154617 62 0.121330724 OS =Saccharomyces cerevisiae GN = NSR1 PE = 1 SV = 1 V-type proton ATPasesubunit a, vacuolar isoform 0.000308399 2.28587E-05 13.49154617 620.121330724 OS = Saccharomyces cerevisiae GN = VPH1 PE = 1 SV = 34-aminobutyrate aminotransferase OS = Saccharomyces 0.0005564324.1243E-05 13.49154617 64 0.125244618 cerevisiae GN = UGA1 PE = 1 SV = 2Dihydroorotate dehydrogenase OS = Saccharomyces 0.000831161 6.27469E-0513.24624533 65 0.127201566 cerevisiae GN = URA1 PE = 1 SV = 1 Eukaryotictranslation initiation factor 2A 0.000405663 3.06247E-05 13.24624533 660.129158513 OS = Saccharomyces cerevisiae GN = YGR054W PE = 1 SV = 1 60Sribosomal protein L32 OS = Saccharomyces 0.00192197 0.00014783313.00094449 67 0.13111546 cerevisiae GN = RPL32 PE = 1 SV = 1 60Sribosomal protein L15-A OS = Saccharomyces 0.002303041 0.00017883112.87829407 68 0.133072407 cerevisiae GN = RPL15A PE = 1 SV = 3Mitochondrial import receptor subunit TOM70 0.000389569 3.11398E-0512.51034281 69 0.135029354 OS = Saccharomyces cerevisiae (strain YJM789)GN = TOM70 PE = 3 SV = 1 Mitochondrial acidic protein MAM33 0.0009066437.24715E-05 12.51034281 70 0.136986301 OS = Saccharomyces cerevisiae GN= MAM33 PE = 1 SV = 1 H/ACA ribonucleoprotein complex subunit 40.000499387 3.99179E-05 12.51034281 70 0.136986301 OS = Saccharomycescerevisiae GN = CBF5 PE = 1 SV = 1 60S ribosomal protein L8-A OS =Saccharomyces 0.003828248 0.000310574 12.32636718 72 0.140900196cerevisiae GN = RPL8A PE = 1 SV = 4 Eukaryotic translation initiationfactor 2 subunit alpha 0.000771455 6.28987E-05 12.26504197 730.142857143 OS = Saccharomyces cerevisiae GN = SUI2 PE = 1 SV = 1NADPH--cytochrome P450 reductase 0.000348866 2.84439E-05 12.26504197 740.14481409 OS = Saccharomyces cerevisiae GN = NCP1 PE = 1 SV = 3Nucleolar protein 58 OS = Saccharomyces cerevisiae 0.0009216417.66773E-05 12.01974113 75 0.146771037 (strain YJM789) GN = NOP58 PE = 3SV = 1 60S ribosomal protein L14 -B OS = Saccharomyces 0.0034290320.000288224 11.89709071 76 0.148727984 cerevisiae GN = RPL14B PE = 1 SV= 1 Pentafunctional AROM polypeptide OS = Saccharomyces 0.000297332.49918E-05 11.89709071 76 0.148727984 cerevisiae GN = ARO1 PE = 1 SV =1 60S ribosomal protein L8-B OS = Saccharomyces 0.00367754 0.00031071411.8357655 78 0.152641879 cerevisiae GN = RPL8B PE = 1 SV = 3GTP-binding protein RHO1 OS = Saccharomyces 0.001110598 9.43228E-0511.77444029 79 0.154598826 cerevisiae GN = RHO1 PE = 1 SV = 3 Invertase2 OS = Saccharomyces cerevisiae GN = SUC2 0.000424013 3.60113E-0511.77444029 80 0.156555773 PE = 1 SV = 1 Squalene synthase OS =Saccharomyces cerevisiae 0.000497125 4.22207E-05 11.77444029 800.156555773 GN = ERG9 PE = 1 SV = 2 Eukaryotic translation initiationfactor 3 subunit B 0.000577426 4.95569E-05 11.65178987 82 0.160469667 OS= Saccharomyces cerevisiae GN = PRT1 PE = 1 SV = 1 Cytochrome c iso-2 OS= Saccharomyces cerevisiae 0.00200888 0.000174244 11.52913945 830.162426614 GN = CYC7 PE = 1 SV = 1 ATP-dependent permease PDR15 OS =Saccharomyces 0.000146155 1.2677E-05 11.52913945 84 0.164383562cerevisiae GN = PDR15 PE = 1 SV = 1 60S ribosomal protein L28 OS =Saccharomyces 0.001473501 0.000130585 11.28383861 85 0.166340509cerevisiae GN = RPL28 PE = 1 SV = 2 Methionyl-tRNA synthetase,cytoplasmic 0.000287593 2.54871 E-05 11.28383861 86 0.168297456 OS =Saccharomyces cerevisiae GN = MES1 PE = 1 SV = 4 Eukaryotic translationinitiation factor 3 subunit G 0.000790304 7.1595E-05 11.03853777 870.170254403 OS = Saccharomyces cerevisiae GN = TIF35 PE = 1 SV = 1General transcriptional corepressor TUP1 0.000307833 2.78871 E-0511.03853777 88 0.17221135 OS = Saccharomyces cerevisiae GN = TUP1 PE = 1SV = 2 Heat shock protein 42 OS = Saccharomyces cerevisiae 0.0005504725.10016E-05 10.79323693 89 0.174168297 GN = HSP42 PE = 1 SV = 1 60Sribosomal protein L15-B OS = Saccharomyces 0.001842433 0.00017883110.30263526 90 0.176125245 cerevisiae GN = RPL15B PE = 1 SV = 2 40Sribosomal protein S23 OS = Saccharomyces 0.001402798 0.00013615910.30263526 90 0.176125245 cerevisiae GN = RPS23A PE = 1 SV = 1T-complex protein 1 subunit theta OS = Saccharomyces 0.0003648593.54141E-05 10.30263526 92 0.180039139 cerevisiae GN = CCT8 PE = 1 SV =1 26S protease regulatory subunit 8 homolog 0.000485124 4.82358E-0510.05733442 93 0.181996086 OS = Saccharomyces cerevisiae GN = RPT6 PE =1 SV = 4 SDO1-like protein YHR087W OS = Saccharomyces 0.0018287410.000181832 10.05733442 94 0.183953033 cerevisiae GN = YHR087W PE = 1 SV= 1 Mitochondrial escape protein 2 OS = Saccharomyces 0.0002216022.25847E-05 9.812033576 95 0.18590998 cerevisiae GN = YME2 PE = 1 SV = 1Alpha-soluble NSF attachment protein 0.000653179 6.65692E-05 9.81203357695 0.18590998 OS = Saccharomyces cerevisiae GN = SEC17 PE = 1 SV = 4Protein translocation protein SEC63 0.000284375 2.89823E-05 9.81203357695 0.18590998 OS = Saccharomyces cerevisiae GN = SEC63 PE = 1 SV = 2Delta-1-pyrroline-5-carboxylate dehydrogenase, 0.000332526 3.38896E-059.812033576 98 0.191780822 mitochondrial OS = Saccharomyces cerevisiaeGN = PUT2 PE = 1 SV = 2 Polyamine N-acetyltransferase 1 OS =Saccharomyces 0.001928069 0.000198988 9.689383157 99 0.193737769cerevisiae GN = PAA1 PE = 1 SV = 1 40S ribosomal protein S22-B OS =Saccharomyces 0.002893283 0.000298603 9.689383157 99 0.193737769cerevisiae GN = RPS22B PE = 1 SV = 3 Phosphoinositide phosphatase SAC10.000286194 3.07028E-05 9.321431897 101 0.197651663 OS = Saccharomycescerevisiae GN = SAC1 PE = 1 SV = 1 40S ribosomal protein S26-A OS =Saccharomyces 0.001507278 0.0001617 9.321431897 101 0.197651663cerevisiae GN = RPS26A PE = 1 SV = 1 26S proteasome regulatory subunitRPN2 0.000390567 4.18999E-05 9.321431897 101 0.197651663 OS =Saccharomyces cerevisiae GN = RPN2 PE = 1 SV = 4 Translational activatorGCN1 OS = Saccharomyces 6.86049E-05 7.35991E-06 9.321431897 1010.197651663 cerevisiae GN = GCN1 PE = 1 SV = 1Dolichyl-diphosphooligosaccharide--protein 0.000249663 2.67838E-059.321431897 105 0.205479452 glycosyltransferase subunit STT3 OS =Saccharomyces cerevisiae GN = STT3 PE = 1 SV = 21,3-beta-glucanosyltransferase GAS5 0.000392433 4.21001 E-05 9.321431897105 0.205479452 OS = Saccharomyces cerevisiae GN = GAS5 PE = 1 SV = 1Acyl-CoA-binding protein OS = Saccharomyces 0.002023076 0.0002170359.321431897 107 0.209393346 cerevisiae GN = ACB1 PE = 1 SV = 3Tricalbin-1 OS = Saccharomyces cerevisiae GN = TCB1 0.0001483751.63478E-05 9.076131058 108 0.211350294 PE = 1 SV = 1 NADP-specificglutamate dehydrogenase 2 0.000399377 4.4003E-05 9.076131058 1080.211350294 OS = Saccharomyces cerevisiae GN = GDH3 PE = 1 SV = 1Dolichyl-phosphate-mannose--protein 0.00021386 2.35629E-05 9.076131058110 0.215264188 mannosyltransferase 1 OS = Saccharomyces cerevisiae GN =PMT1 PE = 1 SV = 1 Mitochondrial import inner membrane translocase0.001923423 0.000211921 9.076131058 110 0.215264188 subunit TIM10 OS =Saccharomyces cerevisiae GN = MRS11 PE = 1 SV = 1 Ornithinecarbamoyltransferase OS = Saccharomyces 0.000523699 5.77006E-059.076131058 110 0.215264188 cerevisiae GN = ARG3 PE = 1 SV = 1 Putativemagnesium-dependent phosphatase YER134C 0.000943354 0.0001068258.830830219 113 0.221135029 OS = Saccharomyces cerevisiae GN = YER134CPE = 1 SV = 1 Eukaryotic translation initiation factor 4B 0.0003974334.50051 E-05 8.830830219 113 0.221135029 OS = Saccharomyces cerevisiaeGN = TIF3 PE = 1 SV = 1 Mitochondrial escape protein 2 OS =Saccharomyces 0.000199503 2.25917E-05 8.830830219 115 0.225048924cerevisiae (strain YJM789) GN = YME2 PE = 3 SV = 1 Vesicle-associatedmembrane protein-associated protein 0.000716233 8.11059E-05 8.830830219115 0.225048924 SCS2 OS = Saccharomyces cerevisiae GN = SCS2 PE = 1 SV =3 Importin beta SMX1 OS = Saccharomyces cerevisiae 0.0001778832.01434E-05 8.830830219 115 0.225048924 GN = SXM1 PE = 1 SV = 1Inorganic phosphate transport protein PHO88 0.000912311 0.000103318.830830219 115 0.225048924 OS = Saccharomyces cerevisiae GN = PHO88 PE= 1 SV = 1 Transcription elongation factor SPT6 0.000225986 2.5951 E-058.708179799 119 0.232876712 OS = Saccharomyces cerevisiae GN = SPT6 PE =1 SV = 1 T-complex protein 1 subunit delta OS = Saccharomyces0.000325467 3.79088E-05 8.585529379 120 0.234833659 cerevisiae GN = CCT4PE = 1 SV = 2 5′-3′ exoribonuclease 1 OS = Saccharomyces cerevisiae0.0002137 2.48907E-05 8.585529379 120 0.234833659 GN = KEM1 PE = 1 SV =1 Fumarate reductase OS = Saccharomyces cerevisiae 0.0003687434.29494E-05 8.585529379 122 0.238747554 GN = YEL047C PE = 1 SV = 13-hydroxy-3-methylglutaryl-coenzyme A reductase 1 0.0001575131.88859E-05 8.34022854 123 0.240704501 OS = Saccharomyces cerevisiae GN= HMG1 PE = 1 SV = 1 26S proteasome regulatory subunit RPN9 0.0003977894.76952E-05 8.34022854 123 0.240704501 OS = Saccharomyces cerevisiae GN= RPN9 PE = 1 SV = 1 Dolichyl-phosphate-mannose--protein 0.0002096522.51375E-05 8.34022854 123 0.240704501 mannosyltransferase 2 OS =Saccharomyces cerevisiae GN = PMT2 PE = 1 SV = 2 Bifunctional proteinGAL10 OS = Saccharomyces 0.006432474 0.000781936 8.226338864 1260.246575342 cerevisiae GN = GAL10 PE = 1 SV = 2 ATP-dependent bile acidpermease OS = Saccharomyces 9.3446E-05 1.15438E-05 8.0949277 1270.24853229 cerevisiae GN = YBT1 PE = 1 SV = 2 Saccharopine dehydrogenase[NAD+, L-lysine-forming] 0.000426308 5.26636E-05 8.0949277 1270.24853229 OS = Saccharomyces cerevisiae GN = LYS1 PE = 1 SV = 3Coatomer subunit gamma OS = Saccharomyces 0.000163509 2.08302E-057.849626861 129 0.252446184 cerevisiae GN = SEC21 PE = 1 SV = 2 Celldivision control protein 53 OS = Saccharomyces 0.000182456 2.3244E-057.849626861 129 0.252446184 cerevisiae GN = CDC53 PE = 1 SV = 1Rotenone-insensitive NADH-ubiquinone oxidoreductase, 0.0002994043.81424E-05 7.849626861 131 0.256360078 mitochondrial OS = Saccharomycescerevisiae GN = NDI1 PE = 1 SV = 1 Argininosuccinate lyase OS =Saccharomyces cerevisiae 0.000329703 4.20024E-05 7.849626861 1310.256360078 GN = ARG4 PE = 1 SV = 2 Zinc finger protein GIS2 OS =Saccharomyces cerevisiae 0.000970965 0.000127686 7.604326022 1330.260273973 GN = GIS2 PE = 1 SV = 1 Protein kinase MCK1 OS =Saccharomyces cerevisiae 0.000384952 5.06228E-05 7.604326022 1330.260273973 GN = MCK1 PE = 1 SV = 1 Malate dehydrogenase, peroxisomal0.000446552 5.87235E-05 7.604326022 135 0.264187867 OS = Saccharomycescerevisiae GN = MDH3 PE = 1 SV = 3 T-complex protein 1 subunit zeta OS =Saccharomyces 0.000277109 3.6441 E-05 7.604326022 136 0.266144814cerevisiae GN = CCT6 PE = 1 SV = 1 ATP-dependent RNA helicase DBP20.000263443 3.57987E-05 7.359025182 137 0.268101761 OS = Saccharomycescerevisiae GN = DBP2 PE = 1 SV = 1 Cytochrome B pre-mRNA-processingprotein 6 0.000860311 0.000116906 7.359025182 138 0.270058708 OS =Saccharomyces cerevisiae GN = CBP6 PE = 1 SV = 1 Protein DCS2 OS =Saccharomyces cerevisiae 0.000392517 5.33382E-05 7.359025182 1380.270058708 GN = DCS2 PE = 1 SV = 3 Eukaryotic translation initiationfactor 3 subunit A 0.000854379 0.000118738 7.195491289 140 0.273972603OS = Saccharomyces cerevisiae GN = TIF32 PE = 1 SV = 1 Glucose-signalingfactor 2 OS = Saccharomyces 0.000677298 9.521 E-05 7.113724343 1410.27592955 cerevisiae GN = GSF2 PE = 1 SV = 1 Glycerol-3-phosphatedehydrogenase [NAD+] 2, 0.000314327 4.41859E-05 7.113724343 1420.277886497 mitochondrial OS = Saccharomyces cerevisiae GN = GPD2 PE = 1SV = 2 Prohibitin-2 OS = Saccharomyces cerevisiae GN = PHB2 0.0004514956.34682E-05 7.113724343 142 0.277886497 PE = 1 SV = 2 40S ribosomalprotein S29-A OS = Saccharomyces 0.002332289 0.000327858 7.113724343 1420.277886497 cerevisiae GN = RPS29A PE = 1 SV = 3 DNA-directed RNApolymerase I subunit RPA1 8.33248E-05 1.17132E-05 7.113724343 1450.283757339 OS = Saccharomyces cerevisiae GN = RPA1 PE = 1 SV = 2Protein transport protein SEC24 OS = Saccharomyces 0.0001498932.10709E-05 7.113724343 145 0.283757339 cerevisiae GN = SEC24 PE = 1 SV= 1 Carboxypeptidase Y OS = Saccharomyces cerevisiae 0.0002508043.65156E-05 6.868423503 147 0.287671233 GN = PRC1 PE = 1 SV = 1 V-typeproton ATPase subunit d OS = Saccharomyces 0.000376931 5.48789E-056.868423503 148 0.28962818 cerevisiae GN = VMA6 PE = 1 SV = 2Uncharacterized protein YJL171C OS = Saccharomyces 0.0003486965.0768E-05 6.868423503 148 0.28962818 cerevisiae GN = YJL171C PE = 1 SV= 1 Vacuolar protein sorting/targeting protein PEP1 8.43666E-051.22833E-05 6.868423503 148 0.28962818 OS = Saccharomyces cerevisiae GN= PEP1 PE = 1 SV = 1 FACT complex subunit POB3 OS = Saccharomyces0.000238097 3.46655E-05 6.868423503 151 0.295499022 cerevisiae GN = POB3PE = 1 SV = 1 Uncharacterized mitochondrial membrane protein 0.0005415027.88393E-05 6.868423503 151 0.295499022 FMP10 OS = Saccharomycescerevisiae GN = FMP10 PE = 1 SV = 1 RNA annealing protein YRA1 OS =Saccharomyces 0.000579546 8.75034E-05 6.623122664 153 0.299412916cerevisiae GN = YRA1 PE = 1 SV = 2 Mitochondrial outer membrane proteinOM45 0.000324421 4.8983E-05 6.623122664 154 0.301369863 OS =Saccharomyces cerevisiae GN = OM45 PE = 1 SV = 2 Mitochondrial importreceptor subunit TOM5 0.002416716 0.000364891 6.623122664 1540.301369863 OS = Saccharomyces cerevisiae GN = TOM5 PE = 1 SV = 1T-complex protein 1 subunit alpha OS = Saccharomyces 0.0002391333.61058E-05 6.623122664 156 0.305283757 cerevisiae GN = TCP1 PE = 1 SV =2 Eukaryotic translation initiation factor 1 A 0.0007988 0.0001252476.377821825 157 0.307240705 OS = Saccharomyces cerevisiae GN = TIF11 PE= 1 SV = 1 Protein MSN5 OS = Saccharomyces cerevisiae 9.79948E-051.53649E-05 6.377821825 158 0.309197652 GN = MSN5 PE = 1 SV = 1 Putativefatty aldehyde dehydrogenase HFD1 0.000232197 3.6407E-05 6.377821825 1580.309197652 OS = Saccharomyces cerevisiae GN = HFD1 PE = 1 SV = 1Ergosterol biosynthetic protein 28 OS = Saccharomyces 0.000812780.000127439 6.377821825 158 0.309197652 cerevisiae GN = ERG28 PE = 1 SV= 1 Protein YRO2 OS = Saccharomyces cerevisiae 0.000359689 5.63969E-056.377821825 158 0.309197652 GN = YRO2 PE = 1 SV = 1Methylene-fatty-acyl-phospholipid synthase 0.000601597 9.43265E-056.377821825 162 0.31702544 OS = Saccharomyces cerevisiae GN = PEM2 PE =1 SV = 1 Protein MKT1 OS = Saccharomyces cerevisiae 0.0001417152.31087E-05 6.132520985 163 0.318982387 GN = MKT1 PE = 1 SV = 2 ProteinMRH1 OS = Saccharomyces cerevisiae 0.000370021 6.03376E-05 6.132520985163 0.318982387 GN = MRH1 PE = 1 SV = 1 Eukaryotic translationinitiation factor 2 subunit beta 0.000424122 6.91596E-05 6.132520985 1650.322896282 OS = Saccharomyces cerevisiae GN = SUI3 PE = 1 SV = 2Peroxiredoxin TSA2 OS = Saccharomyces cerevisiae 0.000594774 0.0001010285.887220146 166 0.324853229 GN = TSA2 PE = 1 SV = 3 Endoplasmicreticulum vesicle protein 25 0.000533314 9.05884E-05 5.887220146 1660.324853229 OS = Saccharomyces cerevisiae GN = ERV25 PE = 1 SV = 1PKHD-type hydroxylase TPA1 OS = Saccharomyces 0.000173629 2.94925E-055.887220146 166 0.324853229 cerevisiae GN = TPA1 PE = 1 SV = 1SED5-binding protein 3 OS = Saccharomyces cerevisiae 0.000123674 2.10071E-05 5.887220146 169 0.33072407 GN = SFB3 PE = 1 SV = 1 D-lactatedehydrogenase [cytochrome] 3 0.000232791 3.95417E-05 5.887220146 1690.33072407 OS = Saccharomyces cerevisiae GN = DLD3 PE = 1 SV = 1Single-stranded nucleic acid-binding protein 0.00076317 0.000132395.764569726 171 0.334637965 OS = Saccharomyces cerevisiae GN = SBP1 PE =1 SV = 2 Protein CW H43 OS = Saccharomyces cerevisiae 0.0001141982.02411E-05 5.641919306 172 0.336594912 GN = CWH43 PE = 1 SV = 2T-complex protein 1 subunit eta OS = Saccharomyces 0.0002062473.65562E-05 5.641919306 172 0.336594912 cerevisiae GN = CCT7 PE = 1 SV =1 26S protease regulatory subunit 6B homolog 0.000256832 4.55221 E-055.641919306 172 0.336594912 OS = Saccharomyces cerevisiae GN = RPT3 PE =1 SV = 1 NADH-cytochrome b5 reductase 1 OS = Saccharomyces 0.0003911956.93372E-05 5.641919306 172 0.336594912 cerevisiae GN = CBR1 PE = 1 SV =2 Glycogen debranching enzyme OS = Saccharomyces 0.000140824 2.49603E-055.641919306 176 0.344422701 cerevisiae GN = GDB1 PE = 1 SV = 1 C-5sterol desaturase OS = Saccharomyces cerevisiae 0.000288325 5.1104E-055.641919306 176 0.344422701 GN = ERG3 PE = 1 SV = 1 13 kDaribonucleoprotein associated protein 0.00090797 0.000160933 5.641919306176 0.344422701 OS = Saccharomyces cerevisiae GN = SNU13 PE = 1 SV = 1UPF0202 protein KRE33 OS = Saccharomyces 0.000103228 1.82965E-055.641919306 176 0.344422701 cerevisiae GN = KRE33 PE = 1 SV = 1 Proteinphosphatase PP2A regulatory subunit A 0.00017364 3.07768E-05 5.641919306176 0.344422701 OS = Saccharomyces cerevisiae GN = TPD3 PE = 1 SV = 2Eukaryotic translation initiation factor 2 subunit gamma 0.0002129123.77375E-05 5.641919306 176 0.344422701 OS = Saccharomyces cerevisiae GN= GCD11 PE = 1 SV = 1 Midasin OS = Saccharomyces cerevisiae GN = MDN12.20277E-05 3.90429E-06 5.641919306 182 0.356164384 PE = 1 SV = 1Galactose-1-phosphate uridylyltransferase 0.005800888 0.0010304165.629654264 183 0.358121331 OS = Saccharomyces cerevisiae GN = GAL7 PE =1 SV = 4 UPF0121 membrane protein YLL023C 0.000366131 6.78446E-055.396618467 184 0.360078278 OS = Saccharomyces cerevisiae GN = YLL023CPE = 1 SV = 1 Phosphatidylinositol transfer protein PDR16 0.0002894445.36342E-05 5.396618467 184 0.360078278 OS = Saccharomyces cerevisiae GN= PDR16 PE = 1 SV = 1 60S ribosomal protein L43 OS = Saccharomyces0.001167888 0.000216411 5.396618467 186 0.363992172 cerevisiae GN =RPL43A PE = 1 SV = 2 Arginine biosynthesis bifunctional protein ARG7,0.000246288 4.56375E-05 5.396618467 186 0.363992172 mitochondrial OS =Saccharomyces cerevisiae GN = ARG7 PE = 1 SV = 1 Probable family 17glucosidase SCW4 0.00029336 5.436E-05 5.396618467 186 0.363992172 OS =Saccharomyces cerevisiae GN = SCW4 PE = 1 SV = 1 26S protease subunitRPT4 OS = Saccharomyces 0.000238513 4.41967E-05 5.396618467 1890.369863014 cerevisiae GN = RPT4 PE = 1 SV = 4 60S ribosomal protein L3OS = Saccharomyces 0.002680969 0.000499055 5.372088383 190 0.371819961cerevisiae GN = RPL3 PE = 1 SV = 4 Phosphoglucomutase-2 OS =Saccharomyces cerevisiae 0.002929237 0.000553804 5.28929935 1910.373776908 GN = PGM2 PE = 1 SV = 1 Uncharacterized phosphatase YNL010W0.000838173 0.000158927 5.273968047 192 0.375733855 OS = Saccharomycescerevisiae GN = YNL010W PE = 1 SV = 1 Elongation factor 3A OS =Saccharomyces cerevisiae 0.004119318 0.000790698 5.209722589 1930.377690802 GN = YEF3 PE = 1 SV = 3 Casein kinase II subunit alpha′ OS =Saccharomyces 0.000285478 5.54184E-05 5.151317628 194 0.37964775cerevisiae GN = CKA2 PE = 1 SV = 2 54S ribosomal protein L12,mitochondrial 0.000544737 0.000105747 5.151317628 194 0.37964775 OS =Saccharomyces cerevisiae GN = MNP1 PE = 1 SV = 1 Nuclear protein SNF4 OS= Saccharomyces cerevisiae 0.000309024 5.99893E-05 5.151317628 1940.37964775 GN = SNF4 PE = 1 SV = 1 Eukaryotic initiation factor 4Fsubunit p150 0.000105031 2.03892E-05 5.151317628 194 0.37964775 OS =Saccharomyces cerevisiae GN = TIF4631 PE = 1 SV = 2 Medium-chain fattyacid ethyl ester synthase/esterase 2 0.000219468 4.26042E-05 5.151317628194 0.37964775 OS = Saccharomyces cerevisiae GN = EHT1 PE = 1 SV = 1 ABCtransporter ATP-binding protein ARB1 0.000164512 3.19359E-05 5.151317628194 0.37964775 OS = Saccharomyces cerevisiae GN = ARB1 PE = 1 SV = 1Cysteinyl-tRNA synthetase OS = Saccharomyces 0.000128513 2.49476E-055.151317628 194 0.37964775 cerevisiae GN = YNL247W PE = 1 SV = 1 ProteinTTP1 OS = Saccharomyces cerevisiae GN = TTP1 0.000165973 3.22195E-055.151317628 194 0.37964775 PE = 1 SV = 1 26S proteasome regulatorysubunit RPN8 0.000293607 5.69966E-05 5.151317628 194 0.37964775 OS =Saccharomyces cerevisiae GN = RPN8 PE = 1 SV = 3 NADH-cytochrome b5reductase 1 OS = Saccharomyces 0.000357999 6.94965E-05 5.151317628 1940.37964775 cerevisiae (strain YJM789) GN = CBR1 PE = 2 SV = 2 ERmembrane protein complex subunit 1 0.000129027 2.50474E-05 5.151317628204 0.399217221 OS = Saccharomyces cerevisiae GN = EMC1 PE = 1 SV = 1Heat shock protein 78, mitochondrial 0.001712467 0.00033471 5.11627465205 0.401174168 OS = Saccharomyces cerevisiae GN = HSP78 PE = 1 SV = 2Nuclear protein STH1/NPS1 OS = Saccharomyces 6.83479E-05 1.39314E-054.906016788 206 0.403131115 cerevisiae GN = STH1 PE = 1 SV = 1mRNA-binding protein PUF3 OS = Saccharomyces 0.000109244 2.22674E-054.906016788 206 0.403131115 cerevisiae GN = PUF3 PE = 1 SV = 1 Actininteracting protein 1 OS = Saccharomyces 0.00015913 3.24356E-054.906016788 206 0.403131115 cerevisiae GN = AIP1 PE = 1 SV = 1Cytochrome c iso -1 OS = Saccharomyces cerevisiae 0.0035176920.000717016 4.906016788 206 0.403131115 GN = CYC1 PE = 1 SV = 2 CTPsynthase 1 OS = Saccharomyces cerevisiae 0.000165559 3.37461 E-054.906016788 206 0.403131115 GN = URA7 PE = 1 SV = 2 Squalenemonooxygenase OS = Saccharomyces 0.000194343 3.96131 E-05 4.906016788206 0.403131115 cerevisiae GN = ERG1 PE = 1 SV = 2 Putative aldehydedehydrogenase-like protein YHR039C 0.000150213 3.06181E-05 4.906016788212 0.414872798 OS = Saccharomyces cerevisiae GN = MSC7 PE = 1 SV = 1Glucosamine--fructose-6-phosphate aminotransferase 0.0005219690.000109122 4.783366368 213 0.416829746 [isomerizing] OS = Saccharomycescerevisiae GN = GFA1 PE = 1 SV = 4 Uncharacterized GTP-binding proteinOLA1 0.001879535 0.000395467 4.752703763 214 0.418786693 OS =Saccharomyces cerevisiae GN = OLA1 PE = 1 SV = 1 Probable1-acyl-sn-glycerol-3-phosphate acyltransferase 0.000300341 6.44409E-054.660715949 215 0.42074364 OS = Saccharomyces cerevisiae GN = SLC1 PE =1 SV = 1 Sporulation-specific protein 21 OS = Saccharomyces 0.0001456443.12494E-05 4.660715949 216 0.422700587 cerevisiae GN = SPO21 PE = 1 SV= 1 Cell division control protein 42 OS = Saccharomyces 0.0004773290.000102415 4.660715949 216 0.422700587 cerevisiae GN = CDC42 PE = 1 SV= 2 Serine/threonine-protein phosphatase PP-Z2 0.000129664 2.78207E-054.660715949 216 0.422700587 OS = Saccharomyces cerevisiae GN = PPZ2 PE =1 SV = 4 Putative mitochondrial carrier protein YHM1/SHM1 0.00030646.57409E-05 4.660715949 216 0.422700587 OS = Saccharomyces cerevisiae GN= YHM1 PE = 1 SV = 1 60S ribosomal protein L24-A OS = Saccharomyces0.001155633 0.000247952 4.660715949 216 0.422700587 cerevisiae GN =RPL24A PE = 1 SV = 1 60S ribosomal protein L35 OS = Saccharomyces0.001463371 0.00031398 4.660715949 216 0.422700587 cerevisiae GN =RPL35A PE = 1 SV = 1 Mitochondrial respiratory chain complexes assembly0.000109111 2.34108E-05 4.660715949 222 0.43444227 protein RCA1 OS =Saccharomyces cerevisiae GN = RCA1 PE = 1 SV = 2 Prohibitin-1 OS =Saccharomyces cerevisiae GN = PHB1 0.000647698 0.00013897 4.660715949222 0.43444227 PE = 1 SV = 2 T-complex protein 1 subunit epsilon0.000164381 3.52695E-05 4.660715949 222 0.43444227 OS = Saccharomycescerevisiae GN = CCT5 PE = 1 SV = 3 Translation machinery-associatedprotein 22 0.000452437 9.70746E-05 4.660715949 222 0.43444227 OS =Saccharomyces cerevisiae (strain YJM789) GN = TMA22 PE = 3 SV = 1 DnaJhomolog 1, mitochondrial OS = Saccharomyces 0.000183181 3.93031 E-054.660715949 222 0.43444227 cerevisiae GN = MDJ1 PE = 1 SV = 1Alpha,alpha-trehalose-phosphate synthase [UDP- 0.000725072 0.0001555714.660715949 222 0.43444227 forming] 56 kDa subunit OS = Saccharomycescerevisiae GN = TPS1 PE = 1 SV = 2 Acetyl coenzymeA synthetase 2 OS =Saccharomyces 0.001617845 0.000347124 4.660715949 222 0.43444227cerevisiae GN = ACS2 PE = 1 SV = 1 60S ribosomal protein L24-B OS =Saccharomyces 0.001159999 0.000248889 4.660715949 222 0.43444227cerevisiae GN = RPL24B PE = 1 SV = 1 Protein YGP1 OS = Saccharomycescerevisiae 0.00027266 5.85018E-05 4.660715949 222 0.43444227 GN = YGP1PE = 1 SV = 2 Actin relatedprotein 2/3 complex subunit 3 0.0004945620.000106113 4.660715949 231 0.452054795 OS = Saccharomyces cerevisiae GN= ARC18 PE = 1 SV = 1 Isoleucyl tRNA synthetase, cytoplasmic 0.0011411470.000248582 4.590629995 232 0.454011742 OS = Saccharomyces cerevisiae GN= ILS1 PE = 1 SV = 1 Eukaryotic translation initiation factor 3 subunitI 0.000511405 0.000112692 4.538065529 233 0.455968689 OS = Saccharomycescerevisiae (strain YJM789) GN = TIF34 PE = 3 SV = 1 Dolichol-phosphatemannosyltransferase 0.001287884 0.000287683 4.476740319 234 0.457925636OS = Saccharomyces cerevisiae GN = DPM1 PE = 1 SV = 3 40S ribosomalprotein S29-B OS = Saccharomyces 0.001433232 0.000324597 4.415415109 2350.459882583 cerevisiae GN = RPS29B PE = 1 SV = 3 Pre-mRNA-splicingfactor ATP-dependent RNA helicase 0.000110115 2.49388E-05 4.415415109236 0.46183953 PRP43 OS = Saccharomyces cerevisiae GN = PRP43 PE = 1 SV= 1 Translocation protein SEC72 OS = Saccharomyces 0.0004462250.000101061 4.415415109 236 0.46183953 cerevisiae GN = SEC72 PE = 1 SV =3 Transcription elongation factor SPT5 0.000166746 3.77645E-054.415415109 236 0.46183953 OS = Saccharomyces cerevisiae GN = SPT5 PE =1 SV = 1 Endoplasmic reticulum transmembrane protein 1 0.0004115579.32092E-05 4.415415109 236 0.46183953 OS = Saccharomyces cerevisiae GN= YET1 PE = 1 SV = 1 Ferrochelatase, mitochondrial OS = Saccharomyces0.000216204 4.89658E-05 4.415415109 236 0.46183953 cerevisiae GN = HEM15PE = 1 SV = 1 Protein CBP3, mitochondrial OS = Saccharomyces 0.0002466965.58715E-05 4.415415109 236 0.46183953 cerevisiae GN = CBP3 PE = 1 SV =1 Putative protein disulfide-isomerase YIL005W 0.000118712 2.68857E-054.415415109 236 0.46183953 OS = Saccharomyces cerevisiae GN = YIL005W PE= 1 SV = 1 Mitochondrial protein import protein MAS5 0.0008633840.000195539 4.415415109 236 0.46183953 OS = Saccharomyces cerevisiae GN= YDJ1 PE = 1 SV = 1 Peroxisomal-coenzyme A synthetase 0.0001594023.61013E-05 4.415415109 236 0.46183953 OS = Saccharomyces cerevisiae GN= FAT2 PE = 1 SV = 1 Nuclear cap-binding protein complex subunit 10.000192799 4.36651 E-05 4.415415109 245 0.479452055 OS = Saccharomycescerevisiae GN = STO1 PE = 1 SV = 2 Proteasome component Y13 OS =Saccharomyces 0.000335781 7.60474E-05 4.415415109 245 0.479452055cerevisiae GN = PRE9 PE = 1 SV = 1 Trehalose synthase complex regulatorysubunit TSL1 0.000304804 7.10041 E-05 4.29276469 247 0.483365949 OS =Saccharomyces cerevisiae GN = TSL1 PE = 1 SV = 1 RibosomalRNA-processing protein 12 6.62221E-05 1.58802E-05 4.17011427 2480.485322896 OS = Saccharomyces cerevisiae GN = RRP12 PE = 1 SV = 1 U3small nucleolar RNA-associated protein 22 6.48185E-05 1.55436E-054.17011427 248 0.485322896 OS = Saccharomyces cerevisiae GN = UTP22 PE =1 SV = 1 40S ribosomal protein S26-B OS = Saccharomyces 0.0013544340.000324795 4.17011427 248 0.485322896 cerevisiae GN = RPS26B PE = 1 SV= 1 Elongator complex protein 1 OS = Saccharomyces 5.95221 E-051.42735E-05 4.17011427 248 0.485322896 cerevisiae GN = IKI3 PE = 1 SV =1 Probable 1,3-beta-glucanosyltransferase GAS3 0.000160338 3.84492E-054.17011427 252 0.493150685 OS = Saccharomyces cerevisiae GN = GAS3 PE =1 SV = 1 Dynamin-related protein DNM1 OS = Saccharomyces 0.0004286610.000102794 4.17011427 252 0.493150685 cerevisiae GN = DNM1 PE = 1 SV =1 Pyruvate dehydrogenase complex protein X component, 0.0004014899.62777E-05 4.17011427 252 0.493150685 mitochondrial OS = Saccharomycescerevisiae GN = PDX1 PE = 1 SV = 1 GTP-binding protein RHO3 OS =Saccharomyces 0.00035976 8.6271E-05 4.17011427 252 0.493150685cerevisiae GN = RHO3 PE = 1 SV = 2 DNA-directed RNA polymerase I subunitRPA2 0.000130225 3.21744E-05 4.04746385 256 0.500978474 OS =Saccharomyces cerevisiae GN = RPA2 PE = 1 SV = 1 54S ribosomal proteinYmL6, mitochondrial 0.000268086 6.83055E-05 3.92481343 257 0.502935421OS = Saccharomyces cerevisiae GN = YML6 PE = 1 SV = 1 ER-derivedvesicles protein ERV29 OS = Saccharomyces 0.000244777 6.23666E-053.92481343 257 0.502935421 cerevisiae GN = ERV29 PE = 1 SV = 1 54Sribosomal protein L3, mitochondrial 0.000194787 4.96296E-05 3.92481343257 0.502935421 OS = Saccharomyces cerevisiae GN = MRPL3 PE = 1 SV = 2Pyrroline-5-carboxylate reductase OS = Saccharomyces 0.0002844497.24746E-05 3.92481343 257 0.502935421 cerevisiae GN = PRO3 PE = 1 SV =1 60S ribosomal protein L34-A OS = Saccharomyces 0.000628399 0.0001601093.92481343 257 0.502935421 cerevisiae GN = RPL34A PE = 1 SV = 1Serine/threonine-protein kinase YPK1 0.000112061 2.85519E-05 3.92481343257 0.502935421 OS = Saccharomyces cerevisiae GN = YPK1 PE = 1 SV = 260S ribosomal protein L19 OS = Saccharomyces 0.000789773 0.0002012263.92481343 257 0.502935421 cerevisiae GN = RP L19A PE = 1 SV = 5CDP-diacylglycerol--inositol 3-phosphatidyltransferase 0.0003452618.79687E-05 3.92481343 264 0.516634051 OS = Saccharomyces cerevisiae GN= PIS1 PE = 1 SV = 1 60S ribosome subunit biogenesis protein NIP70.00042053 0.000107146 3.92481343 264 0.516634051 OS = Saccharomycescerevisiae GN = NIP7 PE = 1 SV = 1 Cell division control protein 10 OS =Saccharomyces 0.00023148 5.89787E-05 3.92481343 264 0.516634051cerevisiae GN = CDC10 PE = 1 SV = 1 E3 ubiquitin-protein ligase RSP5 OS= Saccharomyces 9.33468E-05 2.37837E-05 3.92481343 264 0.516634051cerevisiae GN = RSP5 PE = 1 SV = 1 Glucan 1,3-beta-glucosidase I/II OS=Saccharomyces 0.000167033 4.25582E-05 3.92481343 264 0.516634051cerevisiae GN = EXG1 PE = 1 SV = 1 Eukaryotic translation initiationfactor 5A-2 0.010829628 0.002807121 3.857913202 269 0.526418787 OS =Saccharomyces cerevisiae GN = HYP2 PE = 1 SV = 31,4-alpha-glucan-branching enzyme 0.000204713 5.38413E-05 3.802163011270 0.528375734 OS = Saccharomyces cerevisiae GN = GLC3 PE = 1 SV = 2Polyadenylate-binding protein, cytoplasmic and nuclear 0.0015234840.000407257 3.740837801 271 0.530332681 OS = Saccharomyces cerevisiae GN= PAB1 PE = 1 SV = 4 Protein GCY OS = Saccharomyces cerevisiae GN = GCY10.004153505 0.001120519 3.70676824 272 0.532289628 PE = 1 SV = 1Putative thiosulf ate sulfurtransferase YOR285W 0.001042629 0.0002833613.679512591 273 0.534246575 OS = Saccharomyces cerevisiae GN = YOR285WPE = 1 SV = 1 DNA topoisomerase 2-associated protein PATI 9.07936E-052.46754E-05 3.679512591 274 0.536203523 OS = Saccharomyces cerevisiae GN= PAT1 PE = 1 SV = 3 CAAX prenyl protease 1 OS = Saccharomycescerevisiae 0.000153556 4.17326E-05 3.679512591 274 0.536203523 GN =STE24 PE = 1 SV = 1 Endoplasmic reticulum transmembrane protein 30.000350817 9.53433E-05 3.679512591 274 0.536203523 OS = Saccharomycescerevisiae GN = YET3 PE = 1 SV = 1 ATP-dependent RNA helicase DOB16.58304E-05 1.78911 E-05 3.679512591 277 0.542074364 OS = Saccharomycescerevisiae GN = MTR4 PE = 1 SV = 1 Translation machinery-associatedprotein 17 0.000479086 0.000130204 3.679512591 277 0.542074364 OS =Saccharomyces cerevisiae GN = TMA17 PE = 1 SV = 1 Carboncatabolite-derepressing protein kinase 0.000111525 3.03099E-053.679512591 277 0.542074364 OS = Saccharomyces cerevisiae GN = SNF1 PE =1 SV = 1 tRNA (cytosine-5-)-methyltransferase NCL1 0.0001031742.80402E-05 3.679512591 277 0.542074364 OS = Saccharomyces cerevisiae GN= NCL1 PE = 1 SV = 1 Protein transport protein SEC61 OS = Saccharomyces0.000151778 4.12496E-05 3.679512591 277 0.542074364 cerevisiae GN =SEC61 PE = 1 SV = 1 Calcineurin subunit B OS = Saccharomyces cerevisiae0.000409121 0.000111189 3.679512591 277 0.542074364 GN = CNB1 PE = 1 SV= 3 Lysophospholipase 1 OS = Saccharomyces cerevisiae 0.0001121143.04697E-05 3.679512591 277 0.542074364 GN = PLB1 PE = 1 SV = 2Proteasome component Y7 OS = Saccharomyces 0.000295812 8.03944E-053.679512591 277 0.542074364 cerevisiae GN = PRE8 PE = 1 SV = 1 Metalresistance protein YCF1 OS = Saccharomyces 4.69538E-05 1.27609E-053.679512591 277 0.542074364 cerevisiae GN = YCF1 PE = 1 SV = 2 RanGTPase-activating protein 1 OS = Saccharomyces 0.000175372 4.76619E-053.679512591 277 0.542074364 cerevisiae GN = RNA1 PE = 1 SV = 2L-aminoadipate-semialdehyde dehydrogenase 0.000103446 2.81139E-053.679512591 277 0.542074364 OS = Saccharomyces cerevisiae GN = LYS2 PE =1 SV = 2 Serine hydroxymethyltransferase, mitochondrial 0.0002993298.13501 E-05 3.679512591 288 0.563600783 OS = Saccharomyces cerevisiaeGN = SHM1 PE = 1 SV = 2 Coatomer subunit alpha OS = Saccharomycescerevisiae 0.000351559 9.66186E-05 3.638629118 289 0.56555773 GN = RET1PE = 1 SV = 2 40S ribosomal protein S10-B OS = Saccharomyces 0.0037425630.001028564 3.638629118 289 0.56555773 cerevisiae GN = RPS10B PE = 1 SV= 1 40S ribosomal protein S10-A OS = Saccharomyces 0.0037422690.001028483 3.638629118 289 0.56555773 cerevisiae GN = RPS10A PE = 1 SV= 1 Tryptophan synthase OS = Saccharomyces cerevisiae 0.0004124550.000113995 3.618187381 292 0.571428571 GN = TRP5 PE = 1 SV = 1Serine/threonine-protein phosphatase PP1-2 0.000865225 0.0002432553.556862171 293 0.573385519 OS = Saccharomyces cerevisiae GN = GLC7 PE =1 SV = 1 Aminopeptidase Y OS = Saccharomyces cerevisiae 0.0002583127.26236E-05 3.556862171 293 0.573385519 GN = APE3 PE = 1 SV = 1Glycerol-3-phosphate dehydrogenase [NAD+] 1 0.00143702 0.0004075273.526199566 295 0.577299413 OS = Saccharomyces cerevisiae GN = GPD1 PE =1 SV = 4 Valyl tRNA synthetase, mitochondrial 0.000732554 0.000208353.515978698 296 0.57925636 OS = Saccharomyces cerevisiae GN = VAS1 PE =1 SV = 2 Aconitate hydratase, mitochondrial OS = Saccharomyces0.004316972 0.001227815 3.515978698 297 0.581213307 cerevisiae GN = ACO1PE = 1 SV = 2 Elongation factor Tu, mitochondrial OS = Saccharomyces0.000636478 0.000182083 3.495536962 298 0.583170254 cerevisiae GN = TUF1PE = 1 SV = 1 Glycerol-3-phosphate O-acyltransferase 2 8.96548E-052.61064E-05 3.434211752 299 0.585127202 OS = Saccharomyces cerevisiae GN= GPT2 PE = 1 SV = 1 Putative ribosomal RNA methyltransferase Nop20.000107421 3.12796E-05 3.434211752 299 0.585127202 OS = Saccharomycescerevisiae GN = NOP2 PE = 1 SV = 1 Serine/threonine-protein kinaseYPK2/YKR2 9.78166E-05 2.8483E-05 3.434211752 299 0.585127202 OS =Saccharomyces cerevisiae GN = YPK2 PE = 1 SV = 1 Xanthinephosphoribosyltransferase 1 0.000316809 9.22508E-05 3.434211752 3020.590998043 OS = Saccharomyces cerevisiae GN = XPT1 PE = 1 SV = 13-hydroxy-3-methylglutaryl-coenzyme A reductase 2 6.48202E-051.88748E-05 3.434211752 302 0.590998043 OS = Saccharomyces cerevisiae GN= HMG2 PE = 1 SV = 1 3-keto-steroid reductase OS = Saccharomycescerevisiae 0.000188778 5.49698E-05 3.434211752 302 0.590998043 GN =ERG27 PE = 1 SV = 1 Ras-like protein 2 OS = Saccharomyces cerevisiae0.000216093 6.29235E-05 3.434211752 302 0.590998043 GN = RAS2 PE = 1 SV= 4 Protein phosphatase 1 regulatory subunit SDS22 0.0001928385.6152E-05 3.434211752 302 0.590998043 OS = Saccharomyces cerevisiae GN= SDS22 PE = 1 SV = 1 Ubiquitin-like protein SMT3 OS = Saccharomyces0.001293296 0.000376592 3.434211752 302 0.590998043 cerevisiae GN = SMT3PE = 1 SV = 1 Sphingosine-1-phosphate lyase OS = Saccharomyces0.000114378 3.33055E-05 3.434211752 302 0.590998043 cerevisiae GN = DPL1PE = 1 SV = 1 Protein transport protein SSS1 OS = Saccharomyces0.000838514 0.000244165 3.434211752 302 0.590998043 cerevisiae GN = SSS1PE = 1 SV = 2 UPF0674 endoplasmic reticulum membrane protein 0.0001592424.63692E-05 3.434211752 302 0.590998043 YNR021W OS = Saccharomycescerevisiae GN = YNR021W PE = 1 SV = 3 Non classicalexport protein 2 OS =Saccharomyces 0.000395383 0.000115131 3.434211752 302 0.590998043cerevisiae GN = NCE102 PE = 1 SV = 1 Reduced viability upon starvationprotein 161 0.000247902 7.21859E-05 3.434211752 302 0.590998043 OS =Saccharomyces cerevisiae GN = RVS161 PE = 1 SV = 1 Cytochrome b5 OS =Saccharomyces cerevisiae 0.000563995 0.000164228 3.434211752 3020.590998043 GN = CYB5 PE = 1 SV = 2 60S ribosomal protein L37-A OS =Saccharomyces 0.00076134 0.000221693 3.434211752 302 0.590998043cerevisiae GN = RPL37A PE = 1 SV = 2 Calmodulin OS = Saccharomycescerevisiae GN = CMD1 0.000464783 0.000135339 3.434211752 302 0.590998043PE = 1 SV = 1 Actin relatedprotein 2/3 complex subunit 5 0.0004376820.000127447 3.434211752 302 0.590998043 OS = Saccharomyces cerevisiae GN= ARC15 PE = 1 SV = 1 Mitochondrial outer membrane protein SCY_33929.17107E-05 2.6705E-05 3.434211752 317 0.62035225 OS = Saccharomycescerevisiae (strain YJM789) GN = SCY_3392 PE = 3 SV = 1 tRNApseudouridine synthase 1 OS = Saccharomyces 0.000120677 3.51396E-053.434211752 317 0.62035225 cerevisiae GN = PUS1 PE = 1 SV = 1Heterotrimeric G protein gamma subunit GPG1 0.00050257 0.0001463423.434211752 317 0.62035225 OS = Saccharomyces cerevisiae GN = GPG1 PE =1 SV = 1 Anthranilate synthase component 1 OS = Saccharomyces0.000132104 3.84672E-05 3.434211752 320 0.626223092 cerevisiae GN = TRP2PE = 1 SV = 4 UPF0662 protein YPL260W OS = Saccharomyces 0.0002303716.95657E-05 3.311561332 321 0.628180039 cerevisiae GN = YPL260W PE = 1SV = 1 NADPH-dependent 1-acyldihydroxyacetone phosphate 0.0004407490.000133094 3.311561332 321 0.628180039 reductase OS = Saccharomycescerevisiae GN = AYR1 PE = 1 SV = 1 Long-chain-fatty-acid--CoA ligase 1OS = Saccharomyces 0.000557224 0.000168266 3.311561332 323 0.632093933cerevisiae GN = FAA1 PE = 1 SV = 1 Small COPII coat GTPase SAR10S =Saccharomyces 0.001323495 0.0004072 3.250236122 324 0.634050881cerevisiae GN = SAR1 PE = 1 SV = 1 GMP synthase [glutamine-hydrolyzing]0.000485453 0.000149359 3.250236122 325 0.636007828 OS = Saccharomycescerevisiae GN = GUA1 PE = 1 SV = 4 Mitochondrial outer membrane proteinporin 1 0.003256725 0.001004705 3.241475378 326 0.637964775 OS =Saccharomyces cerevisiae GN = POR1 PE = 1 SV = 4 ATP-dependent helicaseNAM7 OS = Saccharomyces 6.36357E-05 1.99553E-05 3.188910912 3270.639921722 cerevisiae GN = NAM7 PE = 1 SV = 1 Proteasome component PRE2OS = Saccharomyces 0.000220117 6.90258E-05 3.188910912 327 0.639921722cerevisiae GN = PRE2 PE = 1 SV = 3 Homocitrate synthase, mitochondrial0.000859811 0.000269625 3.188910912 327 0.639921722 OS = Saccharomycescerevisiae GN = LYS21 PE = 1 SV = 1 Nucleolar complex protein 2 OS =Saccharomyces 8.53356E-05 2.67601 E-05 3.188910912 330 0.645792564cerevisiae GN = NOC2 PE = 1 SV = 2 Transcriptional regulatory proteinSIN3 3.9829E-05 1.24898E-05 3.188910912 330 0.645792564 OS =Saccharomyces cerevisiae GN = SIN3 PE = 1 SV = 2 Ribosome biogenesisprotein ERB1 7.59361 E-05 2.38126E-05 3.188910912 330 0.645792564 OS =Saccharomyces cerevisiae (strain YJM789) GN = ERB1 PE = 3 SV = 1Dihydroxy-acid dehydratase, mitochondrial 0.000664668 0.0002084313.188910912 330 0.645792564 OS = Saccharomyces cerevisiae GN = ILV3 PE =1 SV = 2 Uncharacterized protein YKL054C OS = Saccharomyces 8.29339E-052.6007E-05 3.188910912 330 0.645792564 cerevisiae GN = YKL054C PE = 1 SV= 1 DNA-directed RNA polymerases I, II, and III subunit 0.0008412440.000263803 3.188910912 330 0.645792564 RPABC5 OS = Saccharomycescerevisiae GN = RPB10 PE = 1 SV = 2 Mitochondrial presequence protease0.000124148 3.89313E-05 3.188910912 330 0.645792564 OS = Saccharomycescerevisiae GN = CYM1 PE = 1 SV = 2 Amidophosphoribosyltransferase OS =Saccharomyces 0.000122775 3.85005E-05 3.188910912 330 0.645792564cerevisiae GN = ADE4 PE = 1 SV = 2 Protein ERP1 OS = Saccharomycescerevisiae 0.000281662 8.83256E-05 3.188910912 330 0.645792564 GN = ERP1PE = 1 SV = 1 Hsp90 co-chaperone HCH1 OS = Saccharomyces 0.0004037750.000126618 3.188910912 330 0.645792564 cerevisiae GN = HCH1 PE = 1 SV =1 Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae 0.0012238720.00038379 3.188910912 330 0.645792564 GN = FAS3 PE = 1 SV = 2Mitochondrial outer membrane protein IML2 8.43558E-05 2.64528E-053.188910912 330 0.645792564 OS = Saccharomyces cerevisiae (strainYJM789) GN = IML2 PE = 3 SV = 1 Choline-phosphate cytidylyltransferase0.000140944 4.41982E-05 3.188910912 342 0.66927593 OS = Saccharomycescerevisiae GN = PCT1 PE = 1 SV = 2 Nucleosome assembly protein OS =Saccharomyces 0.000145425 4.56032E-05 3.188910912 342 0.66927593cerevisiae GN = NAP1 PE = 1 SV = 2 THO complex subunit 2 OS =Saccharomyces cerevisiae 3.78591E-05 1.18721E-05 3.188910912 3420.66927593 GN = THO2 PE = 1 SV = 1 Sec sixty-one protein homolog OS =Saccharomyces 0.000130618 4.096E-05 3.188910912 342 0.66927593cerevisiae GN = SSH1 PE = 1 SV = 1 Cytochrome c heme lyase OS =Saccharomyces 0.000231505 7.25968E-05 3.188910912 342 0.66927593cerevisiae GN = CYC3 PE = 1 SV = 1 Prefoldin subunit 4 OS =Saccharomyces cerevisiae 0.000458719 0.000143848 3.188910912 3420.66927593 GN = GIM3 PE = 1 SV = 1 Gamma-glutamyl phosphate reductase0.000139998 4.39016E-05 3.188910912 342 0.66927593 OS = Saccharomycescerevisiae GN = PRO2 PE = 1 SV = 1 60S ribosomal protein L37-B OS =Saccharomyces 0.000705676 0.000221291 3.188910912 342 0.66927593cerevisiae GN = RPL37B PE = 1 SV = 2 UPF0368 protein YPL225W OS =Saccharomyces 0.000798365 0.000250357 3.188910912 342 0.66927593cerevisiae GN = YPL225W PE = 1 SV = 1Dolichyl-phosphate-mannose--protein 7.91626E-05 2.48243E-05 3.188910912351 0.686888454 mannosyltransferase 4 OS = Saccharomyces cerevisiae GN =PMT4 PE = 1 SV = 1 Increased sodium tolerance protein 2 6.57534E-052.06194E-05 3.188910912 351 0.686888454 OS = Saccharomyces cerevisiae GN= IST2 PE = 1 SV = 1 Glucokinase-1 OS = Saccharomyces cerevisiae0.002234448 0.000709793 3.148027439 353 0.690802348 GN = GLK1 PE = 1 SV= 1 Suppressor protein STM1 OS = Saccharomyces 0.003607455 0.0011648513.096923097 354 0.692759295 cerevisiae GN = STM1 PE = 1 SV = 3 Uridylatekinase OS = Saccharomyces cerevisiae 0.00028029 9.52198E-05 2.943610073355 0.694716243 GN = URA6 PE = 1 SV = 1 Myosin light chain 1 OS =Saccharomyces cerevisiae 0.00078176 0.000265579 2.943610073 3550.694716243 GN = MLC1 PE = 1 SV = 1 Glucose-repressible alcoholdehydrogenase 6.78771 E-05 2.30591 E-05 2.943610073 357 0.698630137transcriptional effector OS = Saccharomyces cerevisiae GN = CCR4 PE = 1SV = 1 54S ribosomal protein L1, mitochondrial 0.000207377 7.04501E-052.943610073 357 0.698630137 OS = Saccharomyces cerevisiae GN = MRPL1 PE= 1 SV = 1 Nuclear polyadenylated RNA-binding protein 3 7.10775E-052.41464E-05 2.943610073 357 0.698630137 OS = Saccharomyces cerevisiae GN= NAB3 PE = 1 SV = 1 Phosphoglycerate mutase 2 OS = Saccharomyces0.000178191 6.05348E-05 2.943610073 357 0.698630137 cerevisiae GN = GPM2PE = 1 SV = 1 3.(45.-bisphosphate nucleotidase OS = Saccharomyces0.000164191 5.57789E-05 2.943610073 357 0.698630137 cerevisiae GN = HAL2PE = 1 SV = 1 Protein SEY1 OS = Saccharomyces cerevisiae (strain7.18829E-05 2.442E-05 2.943610073 357 0.698630137 AWRI1631) GN = SEY1 PE= 3 SV = 1 Thiamine metabolism regulatory protein THI3 9.40228E-053.19413E-05 2.943610073 357 0.698630137 OS = Saccharomyces cerevisiae GN= THI3 PE = 1 SV = 1 Alpha-mannosidase OS = Saccharomyces cerevisiae0.000103261 3.50796E-05 2.943610073 357 0.698630137 GN = AMS1 PE = 1 SV= 2 [NU+] prion formation protein 1 OS = Saccharomyces 4.78514E-051.6256E-05 2.943610073 357 0.698630137 cerevisiae GN = NEW1 PE = 1 SV =1 T-complex protein 1 subunit beta OS = Saccharomyces 0.0001123693.81738E-05 2.943610073 357 0.698630137 cerevisiae GN = CCT2 PE = 1 SV =1 Putative zinc metalloproteinase YIL108W 8.30332E-05 2.8208E-052.943610073 357 0.698630137 OS = Saccharomyces cerevisiae GN = YIL108WPE = 1 SV = 1 Prefoldin subunit 5 OS = Saccharomyces cerevisiae0.000350187 0.000118965 2.943610073 357 0.698630137 GN = GIM5 PE = 1 SV= 1 Probable glycosidase CRH2 OS = Saccharomyces 0.000128804 4.37573E-052.943610073 357 0.698630137 cerevisiae GN = UTR2 PE = 1 SV = 3 Coatomersubunit epsilon OS = Saccharomyces 0.00019001 6.45499E-05 2.943610073357 0.698630137 cerevisiae GN = SEC28 PE = 1 SV = 2 26S proteasomeregulatory subunit RPN13 0.000359064 0.000121981 2.943610073 3570.698630137 OS = Saccharomyces cerevisiae GN = RPN13 PE = 1 SV = 1 40Sribosomal protein S28-A OS = Saccharomyces 0.001693466 0.0005753022.943610073 357 0.698630137 cerevisiae GN = RPS28A PE = 1 SV = 1D-3-phosphoglycerate dehydrogenase 1 0.000125564 4.26565E-05 2.943610073357 0.698630137 OS = Saccharomyces cerevisiae GN = SER3 PE = 1 SV = 1Adenylosuccinate synthetase OS = Saccharomyces 0.000133142 4.52308E-052.943610073 357 0.698630137 cerevisiae GN = ADE12 PE = 1 SV = 3 CTPsynthase 2 OS = Saccharomyces cerevisiae (strain 9.96651E-05 3.38581E-05 2.943610073 375 0.733855186 YJM789) GN = URA8 PE = 3 SV = 1ATP-dependent RNA helicase HAS1 0.000113331 3.85006E-05 2.943610073 3750.733855186 OS = Saccharomyces cerevisiae GN = HAS1 PE = 1 SV = 1 Zincfinger protein ZPR1 OS = Saccharomyces cerevisiae 0.0001167213.96523E-05 2.943610073 375 0.733855186 GN = ZPR1 PE = 1 SV = 1 26Sproteasome regulatory subunit RPN3 0.00010638 3.61393E-05 2.943610073375 0.733855186 OS = Saccharomyces cerevisiae GN = RPN3 PE = 1 SV = 4Peroxisomal membrane protein PMP27 0.000239176 8.12526E-05 2.943610073375 0.733855186 OS = Saccharomyces cerevisiae GN = PEX11 PE = 1 SV = 2Ribose-phosphate pyrophosphokinase 5 0.000120138 4.08132E-05 2.943610073375 0.733855186 OS = Saccharomyces cerevisiae GN = PRS5 PE = 1 SV = 1 U6snRNA-associated Sm-like protein LSm6 0.00068399 0.000232364 2.943610073375 0.733855186 OS = Saccharomyces cerevisiae (strain YJM789) GN = LSM6PE = 3 SV = 1 Protein HMF1 OS = Saccharomyces cerevisiae 0.000462260.000157038 2.943610073 375 0.733855186 GN = HMF1 PE = 1 SV = 1 Generalnegative regulator of transcription subunit 1 2.67455E-05 9.08595E-062.943610073 375 0.733855186 OS = Saccharomyces cerevisiae GN = NOT1 PE =1 SV = 2 Putative glucokinase-2 OS = Saccharomyces cerevisiae0.000881255 0.000312395 2.820959653 384 0.75146771 GN = EMI2 PE = 1 SV =1 26S protease regulatory subunit 4 homolog 0.000252314 8.94425E-052.820959653 385 0.753424658 OS = Saccharomyces cerevisiae GN = RPT2 PE =1 SV = 3 Sphingolipid long chain base-responsive protein LSP10.001589943 0.000573593 2.771899485 386 0.755381605 OS = Saccharomycescerevisiae GN = LSP1 PE = 1 SV = 1 UPF0001 protein YBL036C OS =Saccharomyces 0.000202322 7.4981 E-05 2.698309233 387 0.757338552cerevisiae GN = YBL036C PE = 1 SV = 1 Galactose/lactose metabolismregulatory protein GAL80 0.000121933 4.51887E-05 2.698309233 3880.759295499 OS = Saccharomyces cerevisiae GN = GAL80 PE = 1 SV = 2 U3small nucleolar ribonucleoprotein protein IMP3 0.000269233 9.97785E-052.698309233 388 0.759295499 OS = Saccharomyces cerevisiae GN = IMP3 PE =1 SV = 1 U3 small nucleolar RNA-associated protein 21 5.62287E-052.08385E-05 2.698309233 388 0.759295499 OS = Saccharomyces cerevisiae GN= UTP21 PE = 1 SV = 1 DNA polymerase alpha catalytic subunit A3.53233E-05 1.30909E-05 2.698309233 388 0.759295499 OS = Saccharomycescerevisiae GN = POL1 PE = 1 SV = 2 Probable glycerophosphodiesterphosphodiesterase 0.000158949 5.89071 E-05 2.698309233 388 0.759295499YPL206C OS = Saccharomyces cerevisiae GN = YPL206C PE = 1 SV = 1Cytochrome c oxidase assembly protein COX15 0.000107801 3.99514E-052.698309233 388 0.759295499 OS = Saccharomyces cerevisiae GN = COX15 PE= 1 SV = 1 U6 snRNA associated Sm-like protein LSm5 0.0005653220.00020951 2.698309233 388 0.759295499 OS = Saccharomyces cerevisiae GN= LSM5 PE = 1 SV = 1 60S ribosomal protein L29 OS = Saccharomyces0.000883547 0.000327445 2.698309233 388 0.759295499 cerevisiae GN =RPL29 PE = 1 SV = 3 Tricalbin-3 OS = Saccharomyces cerevisiae GN = TCB36.88849E-05 2.55289E-05 2.698309233 388 0.759295499 PE = 1 SV = 1Peroxiredoxin HYR1 OS = Saccharomyces cerevisiae 0.000632164 0.0002342822.698309233 388 0.759295499 GN = HYR1 PE = 1 SV = 1 Glucose-6-phosphate1 -dehydrogenase 0.000409742 0.000151852 2.698309233 388 0.759295499 OS= Saccharomyces cerevisiae GN = ZWF1 PE = 1 SV = 4 Endosomal proteinP24B OS = Saccharomyces 0.000252541 9.35923E-05 2.698309233 3880.759295499 cerevisiae GN = EMP24 PE = 1 SV = 1 Proteasome component ClOS = Saccharomyces 0.000186846 6.92457E-05 2.698309233 388 0.759295499cerevisiae GN = PRE10 PE = 1 SV = 2 26S proteasome regulatory subunitRPN6 0.000118379 4.38716E-05 2.698309233 388 0.759295499 OS =Saccharomyces cerevisiae GN = RPN6 PE = 1 SV = 3 Monothiolglutaredoxin-3 OS = Saccharomyces cerevisiae 0.000181409 6.72305E-052.698309233 388 0.759295499 GN = GRX3 PE = 1 SV = 1 C-8 sterol isomeraseOS = Saccharomyces cerevisiae 0.000236677 8.77132E-05 2.698309233 3880.759295499 GN = ERG2 PE = 1 SV = 1 Uncharacterized membraneglycoprotein YNR065C 4.70626E-05 1.74415E-05 2.698309233 388 0.759295499OS = Saccharomyces cerevisiae GN = YNR065C PE = 1 SV = 1 Ubiquitincarboxyl-terminal hydrolase 6 0.000103173 3.82361 E-05 2.698309233 4050.792563601 OS = Saccharomyces cerevisiae GN = UBP6 PE = 1 SV = 1Histone chaperone ASF1 OS = Saccharomyces 0.000186452 6.90996E-052.698309233 405 0.792563601 cerevisiae GN = ASF1 PE = 1 SV = 1 Pumiliohomology domain family member 6 0.000156904 5.81491 E-05 2.698309233 4050.792563601 OS = Saccharomyces cerevisiae GN = PUF6 PE = 1 SV = 1Mitochondrial outer membrane protein OM14 0.00040332 0.0001494712.698309233 405 0.792563601 OS = Saccharomyces cerevisiae (strainYJM789) GN = OM14 PE = 3 SV = 1 AP-1 complex subunit gamma-1 OS =Saccharomyces 6.29325E-05 2.33229E-05 2.698309233 405 0.792563601cerevisiae GN = APL4 PE = 1 SV = 1 Signal recognition particle subunitSRP72 8.01207E-05 2.96929E-05 2.698309233 405 0.792563601 OS =Saccharomyces cerevisiae GN = SRP72 PE = 1 SV = 2 Protein transportprotein SEC31 OS = Saccharomyces 4.24814E-05 1.57437E-05 2.698309233 4050.792563601 cerevisiae GN = SEC31 PE = 1 SV = 2 PhosphatidylethanolamineN-methyltransferase 5.8221 E-05 2.15769E-05 2.698309233 405 0.792563601OS = Saccharomyces cerevisiae GN = PEM1 PE = 1 SV = 1 Mitochondrialimport inner membrane translocase 0.000363362 0.000134663 2.698309233405 0.792563601 subunit TIM16 OS = Saccharomyces cerevisiae GN = PAM16PE = 1 SV = 1 Phosphatidate cytidylyltransferase OS = Saccharomyces0.000113698 4.21366E-05 2.698309233 405 0.792563601 cerevisiae GN = CDS1PE = 1 SV = 1 26S proteasome regulatory subunit RPN12 0.0001845896.84093E-05 2.698309233 405 0.792563601 OS = Saccharomyces cerevisiae GN= RPN12 PE = 1 SV = 3 N-terminal acetyltransferase A complex subunitNAT1 5.95728E-05 2.20778E-05 2.698309233 405 0.792563601 OS =Saccharomyces cerevisiae GN = NAT1 PE = 1 SV = 2 Nucleolarpre-ribosomal-associated protein 1 2.89842E-05 1.07416E-05 2.698309233405 0.792563601 OS = Saccharomyces cerevisiae GN = URB1 PE = 1 SV = 2GU4 nucleic-binding protein 1 OS = Saccharomyces 0.001107392 0.0004151192.667646629 418 0.818003914 cerevisiae GN = ARC1 PE = 1 SV = 2Mitochondrial peculiar membrane protein 1 0.000809029 0.0003068012.636984024 419 0.819960861 OS = Saccharomyces cerevisiae GN = MPM1 PE =1 SV = 1 6-phosphogluconate dehydrogenase, decarboxylating 1 0.004942080.001876038 2.63431771 420 0.821917808 OS = Saccharomyces cerevisiae GN= GND1 PE = 1 SV = 1 Transcription-associated protein 1 OS =Saccharomyces 2.59681E-05 1.00821E-05 2.575658814 421 0.823874755cerevisiae GN = TRA1 PE = 1 SV = 1 RNA polymerase-associated proteinCTR9 0.000180474 7.00692E-05 2.575658814 421 0.823874755 OS =Saccharomyces cerevisiae GN = CTR9 PE = 1 SV = 2 DNA-directed RNApolymerases I, II, and III subunit RPABC3 OS = Saccharomyces cerevisiaeGN = RPB8 0.000681273 0.000264504 2.575658814 423 0.82778865 PE = 1 SV =1 Ribonucleoside-diphosphate reductase large chain 1 0.0001129854.38663E-05 2.575658814 423 0.82778865 OS = Saccharomyces cerevisiae GN= RNR1 PE = 1 SV = 2 60S ribosomal protein L10 OS = Saccharomyces0.003548365 0.001377653 2.575658814 423 0.82778865 cerevisiae GN = RPL10PE = 1 SV = 1 Sphingolipid long chain base-responsive protein PILI0.002318695 0.00091108 2.544996209 426 0.833659491 OS = Saccharomycescerevisiae GN = PIL1 PE = 1 SV = 1 Ribosome-associated complex subunitSSZ1 0.001333689 0.000524947 2.540615837 427 0.835616438 OS =Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2 Golgin IMH1 OS =Saccharomyces cerevisiae GN = IMH1 5.09048E-05 2.0752E-05 2.453008394428 0.837573386 PE = 1 SV = 1 Protein SCO2, mitochondrial OS =Saccharomyces 0.000153531 6.25888E-05 2.453008394 428 0.837573386cerevisiae GN = SCO2 PE = 1 SV = 1 3-ketoacyl-CoA reductase OS =Saccharomyces 0.000138384 5.64138E-05 2.453008394 428 0.837573386cerevisiae GN = IFA38 PE = 1 SV = 1 Iron transport multicopper oxidaseFET5 7.55744E-05 3.08089E-05 2.453008394 428 0.837573386 OS =Saccharomyces cerevisiae GN = FET5 PE = 1 SV = 1 Protein ISD11 OS =Saccharomyces cerevisiae 0.000475466 0.00019383 2.453008394 4280.837573386 GN = ISD11 PE = 1 SV = 1 Mitochondrial distribution andmorphology protein 38 8.24018E-05 3.35921 E-05 2.453008394 4280.837573386 OS = Saccharomyces cerevisiae GN = MDM38 PE = 1 SV = 1Elongation of fatty acids protein 3 OS = Saccharomyces 0.0001357285.53313E-05 2.453008394 428 0.837573386 cerevisiae GN = ELO3 PE = 1 SV =1 Nucleolar GTP binding protein 1 OS = Saccharomyces 7.19874E-052.93466E-05 2.453008394 428 0.837573386 cerevisiae GN = NOG1 PE = 1 SV =1 Peptidyl-prolyl cis trans isomerase ESS1 0.000276053 0.0001125372.453008394 428 0.837573386 OS = Saccharomyces cerevisiae GN = ESS1 PE =1 SV = 3 ATPase GET3 OS = Saccharomyces cerevisiae (strain 0.0001361145.54886E-05 2.453008394 428 0.837573386 RM11-1a) GN = GET3 PE = 3 SV = 1Protein APA1 OS = Saccharomyces cerevisiae GN = APA1 0.0001467855.98386E-05 2.453008394 428 0.837573386 PE = 1 SV = 4 Mitochondrialrespiratory chain complexes assembly 6.33584E-05 2.58288E-05 2.453008394439 0.859099804 protein AFG3 OS = Saccharomyces cerevisiae GN = AFG3 PE= 1 SV = 1 Calcium-transporting ATPase 2 OS = Saccharomyces 4.09332E-051.6687E-05 2.453008394 439 0.859099804 cerevisiae GN = PMC1 PE = 1 SV =1 Probable intramembrane protease YKL100C 7.93266E-05 3.23385E-052.453008394 439 0.859099804 OS = Saccharomyces cerevisiae GN = YKL100CPE = 1 SV = 1 KH domain-containing protein YBL032W 0.0001285085.23877E-05 2.453008394 439 0.859099804 OS = Saccharomyces cerevisiae GN= YBL032W PE = 1 SV = 1 Mitochondrial import receptor subunit TOM220.000319029 0.000130056 2.453008394 439 0.859099804 OS = Saccharomycescerevisiae GN = TOM22 PE = 1 SV = 3 Protein MSP1 OS = Saccharomycescerevisiae 0.00013277 5.41252E-05 2.453008394 439 0.859099804 GN = MSP1PE = 1 SV = 2 UPF0364 protein YMR027W OS = Saccharomyces 9.89598E-054.03422E-05 2.453008394 439 0.859099804 cerevisiae GN = YMR027W PE = 1SV = 1 Uncharacterized protein YJL217W OS = Saccharomyces 0.0002438589.94119E-05 2.453008394 439 0.859099804 cerevisiae GN = YJL217W PE = 1SV = 1 ER membrane protein complex subunit 4 0.000249609 0.0001017562.453008394 439 0.859099804 OS = Saccharomyces cerevisiae GN = EMC4 PE =1 SV = 1 Sm-like protein LSml OS = Saccharomyces cerevisiae 0.0002637820.000107534 2.453008394 439 0.859099804 GN = LSM1 PE = 1 SV = 1 Probablealpha-1,6-mannosyltransferase MNN 10 0.000114582 4.6711E-05 2.453008394439 0.859099804 OS = Saccharomyces cerevisiae GN = MNN10 PE = 1 SV = 1Protein HAM1 OS = Saccharomyces cerevisiae 0.000242455 9.884E-052.453008394 439 0.859099804 GN = HAM1 PE = 1 SV = 1 NADPH-dependentmethylglyoxal reductase GRE2 0.000140339 5.7211E-05 2.453008394 4390.859099804 OS = Saccharomyces cerevisiae GN = GRE2 PE = 1 SV = 1 Alpha1,2 mannosyltransferase KTR1 0.000116392 4.74486E-05 2.453008394 4390.859099804 OS = Saccharomyces cerevisiae GN = KTR1 PE = 1 SV = 1Protein VTH1 OS = Saccharomyces cerevisiae GN = VTH1 3.07094E-05 1.25191E-05 2.453008394 453 0.886497065 PE = 1 SV = 1 Trehalose synthasecomplex regulatory subunit TPS3 4.50766E-05 1.8376E-05 2.453008394 4530.886497065 OS = Saccharomyces cerevisiae GN = TPS3 PE = 1 SV = 3 Heatshock protein 60, mitochondrial 0.006551267 0.002731813 2.398138469 4550.890410959 OS = Saccharomyces cerevisiae GN = HSP60 PE = 1 SV = 1Pyruvate dehydrogenase E1 component subunit beta, 0.0010297860.000436161 2.361020579 456 0.892367906 mitochondrial OS = Saccharomycescerevisiae GN = PD B1 PE = 1 SV = 2 Pyruvate dehydrogenase E1 componentsubunit alpha, 0.00110963 0.000471203 2.354888058 457 0.894324853mitochondrial OS = Saccharomyces cerevisiae GN = PDA1 PE = 1 SV = 2Actin relatedprotein 3 OS = Saccharomyces cerevisiae 0.0002054378.81567E-05 2.330357974 458 0.8962818 GN = ARP3 PE = 1 SV = 1 AMPdeaminase OS = Saccharomyces cerevisiae 0.000109083 4.68094E-052.330357974 458 0.8962818 GN = AMD1 PE = 1 SV = 2 Lon protease homolog,mitochondrial 0.000235988 0.000103075 2.289474501 460 0.900195695 OS =Saccharomyces cerevisiae GN = PIM1 PE = 1 SV = 2 Isocitratedehydrogenase [NAD] subunit 1, mitochondrial 0.003037645 0.0013327372.279253633 461 0.902152642 OS = Saccharomyces cerevisiae GN = IDH1 PE =1 SV = 2 Serine hydroxymethyltransferase, cytosolic 0.0011283990.000501825 2.248591028 462 0.904109589 OS = Saccharomyces cerevisiae GN= SHM2 PE = 1 SV = 2 Rab proteins geranylgeranyltransferase component A7.15564E-05 3.24121 E-05 2.207707555 463 0.906066536 OS = Saccharomycescerevisiae GN = MRS6 PE = 1 SV = 2 37S ribosomal protein MRP1,mitochondrial 0.000131255 5.9453E-05 2.207707555 463 0.906066536 OS =Saccharomyces cerevisiae GN = MRP1 PE = 1 SV = 2 Carboxypeptidase S OS =Saccharomyces cerevisiae 7.46309E-05 3.38047E-05 2.207707555 4630.906066536 GN = CPS1 PE = 1 SV = 2 Probable glucose transporter HXT5 OS= Saccharomyces 7.27682E-05 3.2961E-05 2.207707555 466 0.911937378cerevisiae GN = HXT5 PE = 1 SV = 1 Glycerol-3-phosphate dehydrogenase,mitochondrial 0.000665985 0.000301664 2.207707555 466 0.911937378 OS =Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2 Cytochrome b2,mitochondrial OS = Saccharomyces 7.35584E-05 3.33189E-05 2.207707555 4660.911937378 cerevisiae GN = CYB2 PE = 1 SV = 1 Translationmachinery-associated protein 20 0.000237747 0.00010769 2.207707555 4660.911937378 OS = Saccharomyces cerevisiae GN = TMA20 PE = 1 SV = 1D-arabinono-1,4-lactone oxidase OS = Saccharomyces 8.10341E-05 3.67051E-05 2.207707555 466 0.911937378 cerevisiae GN = ALO1 PE = 1 SV = 1Protein phosphatase 2C homolog 3 OS = Saccharomyces 9.38112E-054.24926E-05 2.207707555 466 0.911937378 cerevisiae GN = PTC3 PE = 1 SV =3 DNA-directed RNA polymerase II subunit RPB9 0.000337423 0.0001528392.207707555 466 0.911937378 OS = Saccharomyces cerevisiae GN = RPB9 PE =1 SV = 1 Casein kinase II subunit alpha OS = Saccharomyces 0.0001079284.88868E-05 2.207707555 466 0.911937378 cerevisiae GN = CKA1 PE = 1 SV =1 26S protease regulatory subunit 6A OS = Saccharomyces 9.99044E-054.52526E-05 2.207707555 466 0.911937378 cerevisiae GN = RPT5 PE = 1 SV =3 Enoyl reductase TSC13 OS = Saccharomyces cerevisiae 0.0001311155.93898E-05 2.207707555 466 0.911937378 GN = TSC13 PE = 1 SV = 1 H/ACAribonucleoprotein complex subunit 2 0.000281572 0.000127541 2.207707555466 0.911937378 OS = Saccharomyces cerevisiae GN = NHP2 PE = 1 SV = 2Retrograde regulation protein 2 OS = Saccharomyces 7.35221 E-053.33024E-05 2.207707555 466 0.911937378 cerevisiae GN = RTG2 PE = 1 SV =2 Uncharacterized protein YDR476C OS = Saccharomyces 0.0001908098.64284E-05 2.207707555 466 0.911937378 cerevisiae GN = YDR476C PE = 1SV = 1 DNA-directed RNA polymerases I and III subunit RPAC2 0.0002985040.00013521 2.207707555 466 0.911937378 OS = Saccharomyces cerevisiae GN= RPC19 PE = 1 SV = 1 GPI transamidase component GPI16 7.00996E-053.17522E-05 2.207707555 466 0.911937378 OS = Saccharomyces cerevisiae GN= GPI16 PE = 1 SV = 2 V-type proton ATPase subunit e OS = Saccharomyces0.000575236 0.000260558 2.207707555 466 0.911937378 cerevisiae GN = VMA9PE = 1 SV = 1 Cell division control protein 28 OS = Saccharomyces0.000283067 0.000128217 2.207707555 466 0.911937378 cerevisiae GN =CDC28 PE = 1 SV = 1 Serine/threonine-protein phosphatase 2B catalytic7.03504E-05 3.18658E-05 2.207707555 466 0.911937378 subunit A2 OS =Saccharomyces cerevisiae GN = CNA2 PE = 1 SV = 2 GTP-binding proteinYPT31/YPT8 OS = Saccharomyces 0.000197022 8.92428E-05 2.207707555 4660.911937378 cerevisiae GN = YPT31 PE = 1 SV = 3 FK506-binding nuclearprotein OS = Saccharomyces 0.000103559 4.69079E-05 2.207707555 4660.911937378 cerevisiae GN = FPR3 PE = 1 SV = 2 D-3-phosphoglyceratedehydrogenase 2 9.41815E-05 4.26603E-05 2.207707555 466 0.911937378 OS =Saccharomyces cerevisiae GN = SER33 PE = 1 SV = 1 Coatomer subunit betaOS = Saccharomyces cerevisiae 4.42208E-05 2.00302E-05 2.207707555 4660.911937378 GN = SEC26 PE = 1 SV = 2 Dipeptidyl aminopeptidase B OS =Saccharomyces 5.16141 E-05 2.33791 E-05 2.207707555 466 0.911937378cerevisiae GN = DAP2 PE = 2 SV = 2 Protein UTH1 OS = Saccharomycescerevisiae (strain 0.000131237 5.94449E-05 2.207707555 466 0.911937378RM11-1a) GN = UTH1 PE = 3 SV = 1 Uncharacterized oxidoreductase YML125C0.000136619 6.18829E-05 2.207707555 490 0.95890411 OS = Saccharomycescerevisiae GN = YML125C PE = 1 SV = 1 Long-chain-fatty-acid--CoA ligase3 OS = Saccharomyces 6.18498E-05 2.80154E-05 2.207707555 490 0.95890411cerevisiae GN = FAA3 PE = 1 SV = 1 Actin relatedprotein 2/3 complexsubunit 2 0.000243689 0.000110381 2.207707555 490 0.95890411 OS =Saccharomyces cerevisiae GN = ARC35 PE = 1 SV = 1 Ceramide very longchain fatty acid hydroxylase SCS7 0.000107415 4.86547E-05 2.207707555490 0.95890411 OS = Saccharomyces cerevisiae GN = SCS7 PE = 1 SV = 1Protein SDS24 OS = Saccharomyces cerevisiae (strain 8.43025E-053.81855E-05 2.207707555 490 0.95890411 YJM789) GN = SDS24 PE = 3 SV = 1Cytochrome c oxidase assembly protein COX14 0.000605735 0.0002743732.207707555 490 0.95890411 OS = Saccharomyces cerevisiae GN = COX14 PE =1 SV = 1 Signal recognition particle subunit SRP14 0.0002934280.000132911 2.207707555 490 0.95890411 OS = Saccharomyces cerevisiae GN= SRP14 PE = 1 SV = 1 Putative guanine nucleotide-exchange factor SED44.22602E-05 1.91421E-05 2.207707555 497 0.97260274 OS = Saccharomycescerevisiae GN = SED4 PE = 1 SV = 1 Cytochrome b-c1 complex subunit 1,mitochondrial 0.000757196 0.000347809 2.17704495 498 0.974559687 OS =Saccharomyces cerevisiae GN = COR1 PE = 1 SV = 1 Lysyl-tRNA synthetase,cytoplasmic 0.000693634 0.000321328 2.158647387 499 0.976516634 OS =Saccharomyces cerevisiae GN = KRS1 PE = 1 SV = 2 Glutamyl tRNAsynthetase, cytoplasmic 0.00162997 0.000756317 2.155143089 5000.978473581 OS = Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3Protein transport protein SEC13 OS = Saccharomyces 0.0005674110.000264357 2.146382345 501 0.980430528 cerevisiae GN = SEC13 PE = 1 SV= 1 Threonyl-tRNA synthetase, cytoplasmic 0.000766861 0.000361712.120100112 502 0.982387476 OS = Saccharomyces cerevisiae GN = THS1 PE =1 SV = 2 Uncharacterized protein YMR178W OS = Saccharomyces 0.0008771580.000420688 2.085057135 503 0.984344423 cerevisiae GN = YMR178W PE = 1SV = 1 40S ribosomal protein S25-A OS = Saccharomyces 0.0030254520.001451016 2.085057135 503 0.984344423 cerevisiae GN = RPS25A PE = 1 SV= 1 Transposon Ty2-LR1 Gag-Pol polyprotein 4.50528E-05 2.16075E-052.085057135 503 0.984344423 OS = Saccharomyces cerevisiae GN = TY2B-LR1PE = 3 SV = 1 Farnesyl pyrophosphate synthase OS = Saccharomyces0.001786243 0.000863034 2.069725832 506 0.990215264 cerevisiae GN = FPP1PE = 1 SV = 2 Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial0.002035386 0.000989107 2.057801486 507 0.992172211 OS = Saccharomycescerevisiae GN = IDH2 PE = 1 SV = 1 Nascent polypeptide-associatedcomplex subunit beta-1 0.001038594 0.000513207 2.023731925 5080.994129159 OS = Saccharomyces cerevisiae (strain YJM789) GN = EGD1 PE =3 SV = 1 40S ribosomal protein S3 OS = Saccharomyces 0.005982750.002966283 2.016918013 509 0.996086106 cerevisiae GN = RPS3 PE = 1 SV =5 ATP-dependent RNA helicase SUB2 0.00052204 0.000260592 2.003290188 5100.998043053 OS = Saccharomyces cerevisiae (strain YJM789) GN = SUB2 PE =3 SV = 1 Elongation factor 1-gamma 2 OS = Saccharomyces 0.0011284250.000563286 2.003290188 510 0.998043053 cerevisiae GN = TEF4 PE = 1 SV =1

TABLE 8 Histone PTMs identified from GAL1 promoter chromatin isolatedfrom cells grown in galactose-containing media. Protein SequenceModifications PTM Histone H3 (R)EIAQDFkTDLR(F) Trimethyl (+42) K79me3(R)EIAQDFkTDLR(F) Dimethyl (+28) K79me2 (R)EIAQDFkTDLR(F) Methyl (+14)K79me (R)FQkSTELLIR(K) Acetyl (+42) K56ac (R)KQLASkAAR(K) Acetyl (+42)K23ac (R)kQLASkAAR(K) Acetyl (+42), Acetyl (+42) K18ac K23ac(R)KSTGGkAPR(K) Acetyl (+42) K14ac (R)kSTGGkAPR(K) Acetyl (+42), Acetyl(+42) K9ac K14ac Histone H2B (K)AEkKPASkAPAEK(K) Acetyl (+42), Acetyl(+42) K6ac K11ac (K)KPASkAPAEKkPAAK(K) Acetyl (+42), Acetyl (+42) K11acK17ac (K)APAEKkPAAK(K) Acetyl (+42) K17ac Histone H2A (K)GGkAGSAAK(A)Acetyl (+42) K7ac Histone H4 None Histone H3 Sequence Modifications PTMSpectrum ID (R)EIAQDFkTDLR(F) Trimethyl (+42) K79me3Tackett_051413_L1_21.3892.3892.3.dta (R)EIAQDFkTDLR(F) Trimethyl (+42)Tackett_051413_L1_19.3763.3763.2.dta (R)EIAQDFkTDLR(F) Dimethyl (+28)K79me2 Tackett_051413_L1_21.3948.3948.3.dta (R)EIAQDFkTDLR(F) Dimethyl(+28) Tackett_051413_L1_19.3877.3877.3.dta (R)EIAQDFkTDLR(F) Methyl(+14) K79me Tackett_051413_L1_19.3827.3827.3.dta (R)EIAQDFkTDLR(F)Acetyl (+42) K79ac Tackett_051413_L1_19.3776.3776.3.dta(R)EIAQDFkTDLR(F) Methyl (+14) Tackett_051413_L1_19.3815.3815.2.dta(R)EIAQDFkTDLR(F) Methyl (+14) Tackett_051413_L1_19.3832.3832.2.dta(R)FQkSTELLIR(K) Acetyl (+42) K56ac Tackett_051413_L1_20.5345.5345.2.dta(R)FQkSTELLIR(K) Acetyl (+42) Tackett_051413_L1_19.5128.5128.2.dta(R)FQkSTELLIR(K) Acetyl (+42) Tackett_051413_L1_19.5114.5114.2.dta(R)KQLASkAAR(K) Acetyl (+42) K23ac Tackett_051413_L1_16.1239.1239.2.dta(R)KQLASkAAR(K) Acetyl (+42) Tackett_051413_L1_01.1032.1032.2.dta(R)KQLASkAAR(K) Acetyl (+42) Tackett_051413_L1_20.1311.1311.2.dta(R)KQLASkAAR(K) Acetyl (+42) Tackett_051413_L1_20.1316.1316.2.dta(R)kQLASkAAR(K) Acetyl (+42), K18ac Tackett_051413_L1_19.2100.2100.2.dtaAcetyl (+42) K23ac (R)KQLASkAAR(K) Acetyl (+42)Tackett_051413_L1_19.1327.1327.2.dta (R)KQLASkAAR(K) Acetyl (+42)Tackett_051413_L1_19.1340.1340.2.dta (R)kQLASkAAR(K) Acetyl (+42),Tackett_051413_L1_20.2166.2166.2.dta Acetyl (+42) (R)kQLASkAAR(K) Acetyl(+42), Tackett_051413_L1_20.2178.2178.2.dta Acetyl (+42) (R)KSTGGkAPR(K)Acetyl (+42) K14ac Tackett_051413_L1_20.549.549.2.dta (R)KSTGGkAPR(K)Acetyl (+42) Tackett_051413_L1_23.698.698.2.dta (R)KSTGGkAPR(K) Acetyl(+42) Tackett_051413_L1_22.552.552.2.dta (R)kSTGGkAPR(K) Acetyl (+42),K9ac Tackett_051413_L1_12.1197.1197.2.dta Acetyl (+42) K14ac(R)KSTGGkAPR(K) Acetyl (+42) Tackett_051413_L1_19.506.506.2.dta(R)kSTGGkAPR(K) Acetyl (+42), Tackett_051413_L1_13.1112.1112.2.dtaAcetyl (+42) (R)KSTGGkAPR(K) Acetyl (+42)Tackett_051413_L1_20.438.438.2.dta (R)KSTGGkAPR(K) Acetyl (+42)Tackett_051413_L1_22.555.555.2.dta (R)KSTGGkAPR(K) Acetyl (+42)Tackett_051413_L1_19.623.623.2.dta (R)KSTGGkAPR(K) Acetyl (+42)Tackett_051413_L1_19.627.627.2.dta (K)STGGkAPR(K) Acetyl (+42)Tackett_051413_L1_20.734.734.2.dta (K)STGGkAPR(K) Acetyl (+42)Tackett_051413_L1_19.715.715.2.dta (K)STGGkAPR(K) Acetyl (+42)Tackett_051413_L1_19.720.720.2.dta (K)STGGkAPR(K) Acetyl (+42)Tackett_051413_L1_20.744.744.2.dta (K)STELLIR(K)Tackett_051413_L1_16.3348.3348.2.dta (K)STELLIR(K)Tackett_051413_L1_19.3325.3325.2.dta (K)STELLIR(K)Tackett_051413_L1_20.3349.3349.2.dta

TABLE 9 Proteins enriched with CRISPR-ChAP-MS analysis of GAL1 promoterchromatin in galactose-containing media. Gene Accession gRNA/No gRNAsymbol Number MW (Fold Change) Identified Proteins (transcription)REB1_YEAST DNA-binding protein REB1 OS = Saccharomyces cerevisiae REB1P21538 92 kDa 8.1 GN = REB1 PE = 1 SV = 2 SPT5_YEAST Transcriptionelongation factor SPT5 OS = Saccharomyces SPT5 P27692 116 kDa  5.4cerevisiae GN = SPT5 PE = 1 SV = 1 TOA2_YEAST Transcription initiationfactor IIA small subunit TOA2 P32774 13 kDa 5.1 OS = Saccharomycescerevisiae GN = TOA2 PE = 1 SV = 1 BAF1_YEAST Transcription factor BAF1OS = Saccharomyces cerevisiae BAF1 P14164 82 kDa 4.7 GN = BAF1 PE = 1 SV= 3 SIN3_YEAST Transcriptional regulatory protein SIN3 OS =Saccharomyces SIN3 P22579 175 kDa  4.2 cerevisiae GN = SIN3 PE = 1 SV =2 H2B2_YEAST Histone H2B.2 OS = Saccharomyces cerevisiae GN = HTB2 PE =1 H2B2 P02294 14 kDa 4.1 SV = 2 UME1_YEAST Transcriptional regulatoryprotein UME1 OS = Saccharomyces UME1 Q03010 51 kDa 3.2 cerevisiae GN =UME1 PE = 1 SV = 1 POB3_YEAST FACT complex subunit POB3 OS =Saccharomyces cerevisiae POB3 Q04636 63 kDa 3 GN = POB3 PE = 1 SV = 1RSC6_YEAST Chromatin structure-remodeling complex protein RSC6 RSC6P25632 54 kDa 2.8 OS = Saccharomyces cerevisiae GN = RSC6 PE = 1 SV = 1RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14 RPA14 P50106 15kDa 2.4 OS = Saccharomyces cerevisiae GN = RPA14 PE = 1 SV = 1RSC7_YEAST Chromatin structure-remodeling complex subunit RSC7 RSC7P32832 50 kDa 2.1 OS = Saccharomyces cerevisiae GN = NPL6 PE = 1 SV = 1Identified Proteins (metabolic, ribosomal, common contaminants)PYRF_YEAST Orotidine 5′-phosphate decarboxylase OS = Saccharomyces PYRFP03962 29 kDa 15 cerevisiae GN = URA3 PE = 1 SV = 2 SCW4_YEAST Probablefamily 17 glucosidase SCW4 OS = Saccharomyces SCW4 P53334 40 kDa 15cerevisiae GN = SCW4 PE = 1 SV = 1 RAS2_YEAST Ras-like protein 2 OS =Saccharomyces cerevisiae GN = RAS2 RAS2 P01120 35 kDa 12 PE = 1 SV = 4PWP1_YEAST Periodic tryptophan protein 1 OS = Saccharomyces cerevisiaePWP1 P21304 64 kDa 11 GN = PWP1 PE = 1 SV = 1 ERG19_YEASTDiphosphomevalonate decarboxylase OS = Saccharomyces ERG19 P32377 44 kDa9.6 cerevisiae GN = ERG19 PE = 1 SV = 2 KEL1_YEAST Kelchrepeat-containing protein 1 OS = Saccharomyces cerevisiae KEL1 P38853131 kDa  9.6 GN = KEL1 PE = 1 SV = 1 BGL2_YEAST Glucan1,3-beta-glucosidase OS = Saccharomyces cerevisiae BGL2 P15703 34 kDa9.3 GN = BGL2 PE = 1 SV = 1 SCW10_YEAST Probable family 17 glucosidaseSCW10 OS = Saccharomyces SCW10 Q04951 40 kDa 7.2 cerevisiae GN = SCW10PE = 1 SV = 1 FKBP2_YEAST FK506-binding protein 2 OS = Saccharomycescerevisiae FKBP2 P32472 14 kDa 6 GN = FKB2 PE = 1 SV = 1 YKH7_YEASTUncharacterized protein YKL077W OS = Saccharomyces YKH7 P36081 46 kDa 6cerevisiae GN = YKL077W PE = 1 SV = 1 BRX1_YEAST Ribosome biogenesisprotein BRX1 OS = Saccharomyces BRX1 Q08235 34 kDa 5.8 cerevisiae GN =BRX1 PE = 1 SV = 1 PAL1_YEAST Uncharacterized protein YDR348C OS =Saccharomyces PAL1 Q05518 55 kDa 5.8 cerevisiae GN = YDR348C PE = 1 SV =1 KPR1_YEAST Ribose-phosphate pyrophosphokinase 1 OS = SaccharomycesKPR1 P32895 47 kDa 5 cerevisiae GN = PRS1 PE = 1 SV = 1 YM11_YEASTUncharacterized protein YMR124W OS = Saccharomyces YM11 P39523 106 kDa 5 cerevisiae GN = YMR124W PE = 1 SV = 2 PRS7_YEAST 26S proteaseregulatory subunit 7 homolog OS = Saccharomyces PRS7 P33299 52 kDa 5cerevisiae GN = RPT1 PE = 1 SV = 1 RRP9_YEAST Ribosomal RNA-processingprotein 9 OS = Saccharomyces RRP9 Q06506 65 kDa 5 cerevisiae GN = RRP9PE = 1 SV = 1 CIC1_YEAST Proteasome-interacting protein CIC1 OS =Saccharomyces CIC1 P38779 43 kDa 4.7 cerevisiae GN = CIC1 PE = 1 SV = 1MPM1_YEAST Mitochondrial peculiar membrane protein 1 OS = SaccharomycesMPM1 P40364 28 kDa 4 cerevisiae GN = MPM1 PE = 1 SV = 1 IDI1_YEASTIsopentenyl-diphosphate Delta-isomerase OS = Saccharomyces IDI1 P1549633 kDa 3.9 cerevisiae GN = IDI1 PE = 1 SV = 2 PEX14_YEAST Peroxisomalmembrane protein PEX14 OS = Saccharomyces PEX14 P53112 38 kDa 3.6cerevisiae GN = PEX14 PE = 1 SV = 1 YER0_YEAST Uncharacterized proteinYER080W OS = Saccharomyces YER0 P40053 72 kDa 3.5 cerevisiae GN =YER080W PE = 1 SV = 1 RT23_YEAST 37S ribosomal protein S23,mitochondrial OS = Saccharomyces RT23 Q01163 56 kDa 3.3 cerevisiae GN =RSM23 PE = 1 SV = 2 BUD21_YEAST Bud site selection protein 21 OS =Saccharomyces cerevisiae BUD21 Q08492 24 kDa 3.2 GN = BUD21 PE = 1 SV =1 ELOC_YEAST Elongin-C OS = Saccharomyces cerevisiae GN = ELC1 PE = 1ELOC Q03071 11 kDa 3.2 SV = 1 CDC11_YEAST Cell division control protein11 OS = Saccharomyces cerevisiae CDC11 P32458 48 kDa 3.1 GN = CDC11 PE =1 SV = 1 RFC2_YEAST Replication factor C subunit 2 OS = Saccharomycescerevisiae RFC2 P40348 40 kDa 3.1 GN = RFC2 PE = 1 SV = 1 EFTU_YEASTElongation factor Tu, mitochondrial OS = Saccharomyces EFTU P02992 48kDa 3 cerevisiae GN = TUF1 PE = 1 SV = 1 PPN1_YEAST EndopolyphosphataseOS = Saccharomyces cerevisiae PPN1 Q04119 78 kDa 3 GN = PPN1 PE = 1 SV =1 ETFA_YEAST Probable electron transfer flavoprotein subunit alpha, ETFAQ12480 37 kDa 3 mitochondrial OS = Saccharomyces cerevisiae GN = AIM45PE = 1 SV = 1 GBG_YEAST Guanine nucleotide-binding protein subunit gammaGBG P18852 13 kDa 3 OS = Saccharomyces cerevisiae GN = STE18 PE = 1 SV =1 PUR4_YEAST Phosphoribosylformylglycinamidine synthase PUR4 P38972 149kDa 3 OS = Saccharomyces cerevisiae GN = ADE6 PE = 1 SV = 2 SUCB_YEASTSuccinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial SUCBP53312 47 kDa 2.9 OS = Saccharomyces cerevisiae GN = LSC2 PE = 1 SV = 1UTP15_YEAST U3 small nucleolar RNA-associated protein 15 UTP15 Q04305 58kDa 2.9 OS = Saccharomyces cerevisiae GN = UTP15 PE = 1 SV = 1SEC3_YEAST Exocyst complex component SEC3 OS = Saccharomyces SEC3 P33332155 kDa  2.9 cerevisiae GN = SEC3 PE = 1 SV = 1 AML1_YEASTN(6)-adenine-specific DNA methyltransferase-like 1 AML1 P53200 29 kDa2.9 OS = Saccharomyces cerevisiae GN = AML1 PE = 1 SV = 2 RM10_YEAST 54Sribosomal protein L10, mitochondrial OS = Saccharomyces RM10 P36520 36kDa 2.9 cerevisiae GN = MRPL10 PE = 1 SV = 2 UCRI_YEAST Cytochrome b-c1complex subunit Rieske, mitochondrial UCRI P08067 23 kDa 2.8 OS =Saccharomyces cerevisiae GN = RIP1 PE = 1 SV = 1 KHSE_YEAST Homoserinekinase OS = Saccharomyces cerevisiae GN = THR1 KHSE P17423 39 kDa 2.8 PE= 1 SV = 4 SMD1_YEAST Small nuclear ribonucleoprotein Sm D1 OS =Saccharomyces SMD1 Q02260 16 kDa 2.8 cerevisiae GN = SMD1 PE = 1 SV = 1CYC1_YEAST Cytochrome c iso-1 OS = Saccharomyces cerevisiae GN = CYC1CYC1 P00044 12 kDa 2.6 PE = 1 SV = 2 PET10_YEAST Protein PET10 OS =Saccharomyces cerevisiae GN = PET10 PET10 P36139 31 kDa 2.6 PE = 1 SV =3 RT35_YEAST 37S ribosomal protein S35, mitochondrial OS = SaccharomycesRT35 P53292 40 kDa 2.6 cerevisiae GN = MRPS35 PE = 1 SV = 1 PROF_YEASTProfilin OS = Saccharomyces cerevisiae GN = PFY1 PE = 1 SV = 2 PROFP07274 14 kDa 2.6 NOP13_YEAST Nucleolar protein 13 OS = Saccharomycescerevisiae NOP13 P53883 46 kDa 2.6 GN = NOP13 PE = 1 SV = 1 RM27_YEAST54S ribosomal protein L27, mitochondrial OS = Saccharomyces RM27 P3652616 kDa 2.6 cerevisiae GN = MRPL27 PE = 1 SV = 2 YHA8_YEASTUncharacterized transporter YHL008C OS = Saccharomyces YHA8 P38750 70kDa 2.6 cerevisiae GN = YHL008C PE = 1 SV = 1 DYL1_YEAST Dynein lightchain 1, cytoplasmic OS = Saccharomyces cerevisiae DYL1 Q02647 10 kDa2.5 GN = DYN2 PE = 1 SV = 1 CDC73_YEAST Cell division control protein 73OS = Saccharomyces cerevisiae CDC73 Q06697 44 kDa 2.5 GN = CDC73 PE = 1SV = 1 HRB1_YEAST Protein HRB1 OS = Saccharomyces cerevisiae GN = HRB1PE = 1 HRB1 P38922 52 kDa 2.5 SV = 2 SNZ1_YEAST Pyridoxine biosynthesisprotein SNZ1 OS = Saccharomyces SNZ1 Q03148 32 kDa 2.5 cerevisiae GN =SNZ1 PE = 1 SV = 1 RS9A_YEAST 40S ribosomal protein S9-A OS =Saccharomyces cerevisiae RS9A O13516 22 kDa 2.4 GN = RPS9A PE = 1 SV = 3ARPC2_YEAST Actin-related protein 2/3 complex subunit 2 ARPC2 P53731 40kDa 2.4 OS = Saccharomyces cerevisiae GN = ARC35 PE = 1 SV = 1TRS31_YEAST Transport protein particle 31 kDa subunit OS = SaccharomycesTRS31 Q03337 32 kDa 2.4 cerevisiae GN = TRS31 PE = 1 SV = 1 PUT2_YEASTDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial PUT2 P0727564 kDa 2.4 OS = Saccharomyces cerevisiae GN = PUT2 PE = 1 SV = 2RM51_YEAST 54S ribosomal protein L51, mitochondrial OS = SaccharomycesRM51 Q06090 16 kDa 2.4 cerevisiae GN = MRPL51 PE = 1 SV = 1 LGUL_YEASTLactoylglutathione lyase OS = Saccharomyces cerevisiae LGUL P50107 37kDa 2.4 GN = GLO1 PE = 1 SV = 1 HIS8_YEAST Histidinol-phosphateaminotransferase OS = Saccharomyces HIS8 P07172 43 kDa 2.3 cerevisiae GN= HIS5 PE = 1 SV = 2 NPT1_YEAST Nicotinate phosphoribosyltransferase OS= Saccharomyces NPT1 P39683 49 kDa 2.3 cerevisiae GN = NPT1 PE = 1 SV =3 METK2_YEAST S-adenosylmethionine synthase 2 OS = Saccharomyces METK2P19358 42 kDa 2.2 cerevisiae GN = SAM2 PE = 1 SV = 3 FMP10_YEASTUncharacterized mitochondrial membrane protein FMP10 FMP10 P40098 28 kDa2.2 OS = Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1 YPT31_YEASTGTP-binding protein YPT31/YPT8 OS = Saccharomyces YPT31 P38555 24 kDa2.2 cerevisiae GN = YPT31 PE = 1 SV = 3 (+1) YMX6_YEAST Uncharacterizedprotein YMR086W OS = Saccharomyces YMX6 Q04279 106 kDa 2.2 cerevisiae GN= YMR086W PE = 1 SV = 1 ACPM_YEAST Acyl carrier protein, mitochondrialOS = Saccharomyces ACPM P32463 14 kDa 2.2 cerevisiae GN = ACP1 PE = 1 SV= 1 RM33_YEAST 54S ribosomal protein L33, mitochondrial OS =Saccharomyces RM33 P20084 10 kDa 2.2 cerevisiae GN = MRPL33 PE = 1 SV =4 RL14A_YEAST 60S ribosomal protein L14-A OS = Saccharomyces cerevisiaeRL14A P36105 15 kDa 2.1 GN = RPL14A PE = 1 SV = 1 PBP1_YEASTPAB1-binding protein 1 OS = Saccharomyces cerevisiae PBP1 P53297 79 kDa2.1 GN = PBP1 PE = 1 SV = 1 GPDM_YEAST Glycerol-3-phosphatedehydrogenase, mitochondrial GPDM P32191 72 kDa 2.1 OS = Saccharomycescerevisiae GN = GUT2 PE = 1 SV = 2 RIB1_YEAST GTP cyclohydrolase-2 OS =Saccharomyces cerevisiae GN = RIB1 RIB1 P38066 38 kDa 2.1 PE = 1 SV = 2OTC_YEAST Ornithine carbamoyltransferase OS = Saccharomyces cerevisiaeOTC P05150 38 kDa 2.1 GN = ARG3 PE = 1 SV = 1 UBP6_YEAST Ubiquitincarboxyl-terminal hydrolase 6 OS = Saccharomyces UBP6 P43593 57 kDa 2.1cerevisiae GN = UBP6 PE = 1 SV = 1 SUR7_YEAST Protein SUR7 OS =Saccharomyces cerevisiae GN = SUR7 PE = 1 SUR7 P54003 34 kDa 2.1 SV = 1TWF1_YEAST Twinfilin-1 OS = Saccharomyces cerevisiae GN = TWF1 PE = 1TWF1 P53250 37 kDa 2.1 SV = 1 RN49_YEAST 54S ribosomal protein L49,mitochondrial OS = Saccharomyces RN49 P40858 18 kDa 2.1 cerevisiae GN =MRPL49 PE = 1 SV = 2 RSM28_YEAST 37S ribosomal protein RSM28,mitochondrial RSM28 Q03430 41 kDa 2.1 OS = Saccharomyces cerevisiae GN =RSM28 PE = 1 SV = 2 1832 protiens were identified and thoseenriched >2-fold (with at least 5 spectral counts) with Cas9-PrA/gRNAverses the no gRNA control are listed (86 proteins). Enrichment wascalculated by normalized NSAF as detailed in Byrum et al., 2013.Protiens are categorized as those involved in transcription (11proteins) and those that are common contaminants (74 proteins) inaffinity purifications (Byrum et al., 2013).

TABLE 10 Spectral counts and normalized NSAF values. gRNA/ SpectralNormalized no counts NSAF gRNA Gene Accession No values (Fold IdentifiedProteins (318) Symbol Number MW gRNA gRNA gRNA No gRNA Change)PYRF_YEAST Orotidine 5′-phosphate PYRF P03962 29 kDa 657 45 2.30340.15574 15 decarboxylase OS = Saccharomyces cerevisiae GN = URA3 PE = 1SV = 2 SCW4_YEAST Probable family 17 SCW4 P53334 40 kDa 43 3 0.113550.0076196 15 glucosidase SCW4 OS = Saccharomyces cerevisiae GN = SCW4 PE= 1 SV = 1 RAS2_YEAST Ras-like protein 2 RAS2 P01120 35 kDa 10 10.030093 0.0025358 12 OS = Saccharomyces cerevisiae GN = RAS2 PE = 1 SV= 4 PWP1_YEAST Periodic tryptophan PWP1 P21304 64 kDa 10 1 0.020540.0019358 11 protein 1 OS = Saccharomyces cerevisiae GN = PWP1 PE = 1 SV= 1 ERG19_YEAST Diphosphomevalonate ERG19 P32377 44 kDa 9 1 0.0221740.0023133 9.6 decarboxylase OS = Saccharomyces cerevisiae GN = ERG19 PE= 1 SV = 2 KEL1_YEAST Kelch repeat-containing KEL1 P38853 131 kDa  6 10.005493 0.00057277 9.6 protein 1 OS = Saccharomyces cerevisiae GN =KEL1 PE = 1 SV = 1 BGL2_YEAST Glucan 1,3-beta- BGL2 P15703 34 kDa 78 100.23854 0.02567 9.3 glucosidase OS = Saccharomyces cerevisiae GN = BGL2PE = 1 SV = 1 REB1_YEAST DNA-binding protein REB1 P21538 92 kDa 5 10.006768 0.00083919 8.1 REB1 OS = Saccharomyces cerevisiae GN = REB1 PE= 1 SV = 2 SCW10_YEAST Probable family 17 SCW10 Q04951 40 kDa 24 30.067308 0.0093606 7.2 glucosidase SCW10 OS = Saccharomyces cerevisiaeGN = SCW10 PE = 1 SV = 1 FKBP2_YEAST FK506-binding protein FKBP2 P3247214 kDa 5 1 0.028788 0.0047652 6 2 OS = Saccharomyces cerevisiae GN =FKB2 PE = 1 SV = 1 YKH7_YEAST Uncharacterized protein YKH7 P36081 46 kDa5 1 0.010224 0.0017008 6 YKL077W OS = Saccharomyces cerevisiae GN =YKL077W PE = 1 SV = 1 BRX1_YEAST Ribosome biogenesis BRX1 Q08235 34 kDa10 2 0.032329 0.0055678 5.8 protein BRX1 OS = Saccharomyces cerevisiaeGN = BRX1 PE = 1 SV = 1 PAL1_YEAST Uncharacterized protein PAL1 Q0551855 kDa 5 1 0.010082 0.0017505 5.8 YDR348C OS = Saccharomyces cerevisiaeGN = YDR348C PE = 1 SV = 1 SPT5_YEAST Transcription elongation SPT5P27692 116 kDa  5 1 0.005671 0.001046 5.4 factor SPT5 OS = Saccharomycescerevisiae GN = SPT5 PE = 1 SV = 1 TOA2_YEAST Transcription initiationTOA2 P32774 13 kDa 5 1 0.026691 0.005273 5.1 factor IIA small subunit OS= Saccharomyces cerevisiae GN = TOA2 PE = 1 SV = 1 KPR1_YEASTRibose-phosphate KPR1 P32895 47 kDa 8 2 0.020962 0.004191 5pyrophosphokinase 1 OS = Saccharomyces cerevisiae GN = PRS1 PE = 1 SV =1 YM11_YEAST Uncharacterized protein YM11 P39523 106 kDa  6 2 0.0070740.001414 5 YMR124W OS = Saccharomyces cerevisiae GN = YMR124W PE = 1 SV= 2 PRS7_YEAST 26S protease regulatory PRS7 P33299 52 kDa 5 1 0.0111320.0022086 5 subunit 7 homolog OS = Saccharomyces cerevisiae GN = RPT1 PE= 1 SV = 1 RRP9_YEAST Ribosomal RNA- RRP9 Q06506 65 kDa 5 1 0.010060.0020314 5 processing protein 9 OS = Saccharomyces cerevisiae GN = RRP9PE = 1 SV = 1 CIC1_YEAST Proteasome-interacting CIC1 P38779 43 kDa 6 10.014793 0.0031713 4.7 protein CIC1 OS = Saccharomyces cerevisiae GN =CIC1 PE = 1 SV = 1 BAF1_YEAST Transcription factor BAF1 P14164 82 kDa 51 0.00721 0.0015254 4.7 BAF1 OS = Saccharomyces cerevisiae GN = BAF1 PE= 1 SV = 3 SIN3_YEAST Transcriptional SIN3 P22579 175 kDa  5 1 0.0037570.00088897 4.2 regulatory protein SIN3 OS = Saccharomyces cerevisiae GN= SIN3 PE = 1 SV = 2 H2B2_YEAST Histone H2B.2 H2B2 P02294 14 kDa 81 870.021748 0.0053125 4.1 OS = Saccharomyces cerevisiae GN = HTB2 PE = 1 SV= 2 MPM1_YEAST Mitochondrial peculiar MPM1 P40364 28 kDa 10 3 0.035950.0090786 4 membrane protein 1 OS = Saccharomyces cerevisiae GN = MPM1PE = 1 SV = 1 IDI1_YEAST Isopentenyl-diphosphate IDI1 P15496 33 kDa 18 50.054499 0.014115 3.9 Delta-isomerase OS = Saccharomyces cerevisiae GN =IDI1 PE = 1 SV = 2 PEX14_YEAST Peroxisomal PEX14 P53112 38 kDa 11 30.032705 0.0090831 3.6 membrane protein PEX14 OS = Saccharomycescerevisiae GN = PEX14 PE = 1 SV = 1 YER0_YEAST Uncharacterized proteinYER0 P40053 72 kDa 11 3 0.018477 0.0052646 3.5 YER080W OS =Saccharomyces cerevisiae GN = YER080W PE = 1 SV = 1 RT23_YEAST 37Sribosomal protein RT23 Q01163 56 kDa 5 2 0.010978 0.0033269 3.3 S23,mitochondrial OS = Saccharomyces cerevisiae GN = RSM23 PE = 1 SV = 2BUD21_YEAST Bud site selection BUD21 Q08492 24 kDa 6 2 0.0232790.0073049 3.2 protein 21 OS = Saccharomyces cerevisiae GN = BUD21 PE = 1SV = 1 UME1_YEAST Transcriptional UME1 Q03010 51 kDa 6 2 0.0148750.0046531 3.2 regulatory protein UME1 OS = Saccharomyces cerevisiae GN =UME1 PE = 1 SV = 1 ELOC_YEAST Elongin-C ELOC Q03071 11 kDa 5 2 0.0414490.012996 3.2 OS = Saccharomyces cerevisiae GN = ELC1 PE = 1 SV = 1CDC11_YEAST Cell division control CDC11 P32458 48 kDa 12 4 0.0330150.010509 3.1 protein 11 OS = Saccharomyces cerevisiae GN = CDC11 PE = 1SV = 1 RFC2_YEAST Replication factor C RFC2 P40348 40 kDa 6 2 0.0141260.0046262 3.1 subunit 2 OS = Saccharomyces cerevisiae GN = RFC2 PE = 1SV = 1 EFTU_YEAST Elongation factor Tu, EFTU P02992 48 kDa 40 140.095198 0.0321 3 mitochondrial OS = Saccharomyces cerevisiae GN = TUF1PE = 1 SV = 1 PPN1_YEAST Endopolyphosphatase PPN1 Q04119 78 kDa 14 50.017319 0.0058652 3 OS = Saccharomyces cerevisiae GN = PPN1 PE = 1 SV =1 POB3_YEAST FACT complex subunit POB3 Q04636 63 kDa 12 4 0.0244820.0082034 3 POB3 OS = Saccharomyces cerevisiae GN = POB3 PE = 1 SV = 1ETFA_YEAST Probable electron ETFA Q12480 37 kDa 11 4 0.027632 0.009349 3transfer flavoprotein subunit alpha, mitochondrial OS = Saccharomycescerevisiae GN = AIM45 PE = 1 SV = 1 GBG_YEAST Guanine nucleotide- GBGP18852 13 kDa 5 2 0.035393 0.011696 3 binding protein subunit gamma OS =Saccharomyces cerevisiae GN = STE18 PE = 1 SV = 1 PUR4_YEAST PUR4 P38972149 kDa  5 2 0.004221 0.0014279 3 Phosphoribosylformylglycinamidinesynthase OS = Saccharomyces cerevisiae GN = ADE6 PE = 1 SV = 2SUCB_YEAST Succinyl-CoA ligase SUCB P53312 47 kDa 27 10 0.0594460.020597 2.9 [ADP-forming] subunit beta, mitochondrial OS =Saccharomyces cerevisiae GN = LSC2 PE = 1 SV = 1 UTP15_YEAST U3 smallnucleolar UTP15 Q04305 58 kDa 8 3 0.01818 0.0063459 2.9 RNA-associatedprotein 15 OS = Saccharomyces cerevisiae GN = UTP15 PE = 1 SV = 1SEC3_YEAST Exocyst complex SEC3 P33332 155 kDa  7 3 0.006023 0.00205592.9 component SEC3 OS = Saccharomyces cerevisiae GN = SEC3 PE = 1 SV = 1AML1_YEAST N(6)-adenine-specific AML1 P53200 29 kDa 5 2 0.0173640.006086 2.9 DNA methyltransferase-like 1 OS = Saccharomyces cerevisiaeGN = AML1 PE = 1 SV = 2 RM10_YEAST 54S ribosomal protein RM10 P36520 36kDa 5 2 0.013874 0.0047367 2.9 L10, mitochondrial OS = Saccharomycescerevisiae GN = MRPL10 PE = 1 SV = 2 UCRI_YEAST Cytochrome b-c1 UCRIP08067 23 kDa 18 7 0.068993 0.024609 2.8 complex subunit Rieske,mitochondrial OS = Saccharomyces cerevisiae GN = RIP1 PE = 1 SV = 1KHSE_YEAST Homoserine kinase KHSE P17423 39 kDa 9 3 0.019995 0.00712712.8 OS = Saccharomyces cerevisiae GN = THR1 PE = 1 SV = 4 SMD1_YEASTSmall nuclear SMD1 Q02260 16 kDa 8 3 0.040301 0.0143 2.8ribonucleoprotein Sm D1 OS = Saccharomyces cerevisiae GN = SMD1 PE = 1SV = 1 RSC6_YEAST Chromatin structure- RSC6 P25632 54 kDa 7 3 0.0158750.00569 2.8 remodeling complex protein RSC6 OS = Saccharomycescerevisiae GN = RSC6 PE = 1 SV = 1 CYC1_YEAST Cytochrome c iso-1 CYC1P00044 12 kDa 117 68 0.61144 0.2352 2.6 OS = Saccharomyces cerevisiae GN= CYC1 PE = 1 SV = 2 PET10_YEAST Protein PET10 PET10 P36139 31 kDa 17 70.048927 0.019041 2.6 OS = Saccharomyces cerevisiae GN = PET10 PE = 1 SV= 3 RT35_YEAST 37S ribosomal protein RT35 P53292 40 kDa 12 5 0.0317110.011999 2.6 S35, mitochondrial OS = Saccharomyces cerevisiae GN =MRPS35 PE = 1 SV = 1 PROF_YEAST Profilin PROF P07274 14 kDa 11 40.058874 0.023044 2.6 OS = Saccharomyces cerevisiae GN = PFY1 PE = 1 SV= 2 NOP13_YEAST Nucleolar protein 13 NOP13 P53883 46 kDa 6 3 0.0170940.0065024 2.6 OS = Saccharomyces cerevisiae GN = NOP13 PE = 1 SV = 1RM27_YEAST 54S ribosomal protein RM27 P36526 16 kDa 5 2 0.0245050.0095335 2.6 L27, mitochondrial OS = Saccharomyces cerevisiae GN =MRPL27 PE = 1 SV = 2 YHA8_YEAST Uncharacterized YHA8 P38750 70 kDa 5 20.009366 0.0036348 2.6 transporter YHL008C OS = Saccharomyces cerevisiaeGN = YHL008C PE = 1 SV = 1 DYL1_YEAST Dynein light chain 1, DYL1 Q0264710 kDa 10 4 0.073508 0.029371 2.5 cytoplasmic OS = Saccharomycescerevisiae GN = DYN2 PE = 1 SV = 1 CDC73_YEAST Cell division controlCDC73 Q06697 44 kDa 9 4 0.018285 0.0073158 2.5 protein 73 OS =Saccharomyces cerevisiae GN = CDC73 PE = 1 SV = 1 HRB1_YEAST ProteinHRB1 HRB1 P38922 52 kDa 9 4 0.020922 0.0084023 2.5 OS = Saccharomycescerevisiae GN = HRB1 PE = 1 SV = 2 SNZ1_YEAST Pyridoxine biosynthesisSNZ1 Q03148 32 kDa 5 3 0.006198 0.0025142 2.5 protein SNZ1 OS =Saccharomyces cerevisiae GN = SNZ1 PE = 1 SV = 1 RS9A_YEAST 40Sribosomal protein RS9A O13516 22 kDa 151 156 0.009155 0.0037905 2.4 S9-AOS = Saccharomyces cerevisiae GN = RPS9A PE = 1 SV = 3 ARPC2_YEASTActin-related protein ARPC2 P53731 40 kDa 15 7 0.044768 0.018359 2.4 2/3complex subunit 2 OS = Saccharomyces cerevisiae GN = ARC35 PE = 1 SV = 1TRS31_YEAST Transport protein TRS31 Q03337 32 kDa 8 4 0.026095 0.0107792.4 particle 31 kDa subunit OS = Saccharomyces cerevisiae GN = TRS31 PE= 1 SV = 1 RPA14_YEAST DNA-directed RNA RPA14 P50106 15 kDa 7 3 0.0365470.01524 2.4 polymerase I subunit RPA14 OS = Saccharomyces cerevisiae GN= RPA14 PE = 1 SV = 1 PUT2_YEAST Delta-1-pyrroline-5- PUT2 P07275 64 kDa6 3 0.012072 0.0051256 2.4 carboxylate dehydrogenase, mitochondrial OS =Saccharomyces cerevisiae GN = PUT2 PE = 1 SV = 2 RM51_YEAST 54Sribosomal protein RM51 Q06090 16 kDa 6 3 0.035158 0.014913 2.4 L51,mitochondrial OS = Saccharomyces cerevisiae GN = MRPL51 PE = 1 SV = 1LGUL_YEAST Lactoylglutathione lyase LGUL P50107 37 kDa 5 2 0.0127640.0053001 2.4 OS = Saccharomyces cerevisiae GN = GLO1 PE = 1 SV = 1HIS8_YEAST Histidinol-phosphate HIS8 P07172 43 kDa 9 5 0.024457 0.0107842.3 aminotransferase OS = Saccharomyces cerevisiae GN = HIS5 PE = 1 SV =2 NPT1_YEAST Nicotinate NPT1 P39683 49 kDa 5 2 0.010476 0.0046279 2.3phosphoribosyltransferase OS = Saccharomyces cerevisiae GN = NPT1 PE = 1SV = 3 METK2_YEAST S-adenosylmethionine METK2 P19358 42 kDa 79 750.038801 0.017378 2.2 synthase 2 OS = Saccharomyces cerevisiae GN = SAM2PE = 1 SV = 3 FMP10_YEAST Uncharacterized FMP10 P40098 28 kDa 14 80.055633 0.0252 2.2 mitochondrial membrane protein FMP10 OS =Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1 YPT31_YEASTGTP-binding protein YPT31 P38555 24 kDa 9 4 0.028763 0.012951 2.2YPT31/YPT8 OS = Saccharomyces (+1) cerevisiae GN = YPT31 PE = 1 SV = 3YMX6_YEAST Uncharacterized protein YMX6 Q04279 106 kDa  8 5 0.0073220.0033862 2.2 YMR086W OS = Saccharomyces cerevisiae GN = YMR086W PE = 1SV = 1 ACPM_YEAST Acyl carrier protein, ACPM P32463 14 kDa 8 4 0.0464870.021428 2.2 mitochondrial OS = Saccharomyces cerevisiae GN = ACP1 PE =1 SV = 1 RM33_YEAST 54S ribosomal protein RM33 P20084 10 kDa 7 30.054493 0.024282 2.2 L33, mitochondrial OS = Saccharomyces cerevisiaeGN = MRPL33 PE = 1 SV = 4 RL14A_YEAST 60S ribosomal protein RL14A P3610515 kDa 111 121 0.010356 0.0050431 2.1 L14-A OS = Saccharomycescerevisiae GN = RPL14A PE = 1 SV = 1 PBP1_YEAST PAB1-binding protein 1PBP1 P53297 79 kDa 32 16 0.050084 0.024091 2.1 OS = Saccharomycescerevisiae GN = PBP1 PE = 1 SV = 1 GPDM_YEAST Glycerol-3-phosphate GPDMP32191 72 kDa 17 8 0.026484 0.012419 2.1 dehydrogenase, mitochondrial OS= Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2 RIB1_YEAST GTPcyclohydrolase-2 RIB1 P38066 38 kDa 16 9 0.043642 0.020754 2.1 OS =Saccharomyces cerevisiae GN = RIB1 PE = 1 SV = 2 RSC7_YEAST Chromatinstructure- RSC7 P32832 50 kDa 13 7 0.029347 0.014198 2.1 remodelingcomplex subunit RSC7 OS = Saccharomyces cerevisiae GN = NPL6 PE = 1 SV =1 OTC_YEAST Ornithine OTC P05150 38 kDa 13 6 0.031697 0.015373 2.1carbamoyltransferase OS = Saccharomyces cerevisiae GN = ARG3 PE = 1 SV =1 UBP6_YEAST Ubiquitin carboxyl- UBP6 P43593 57 kDa 9 5 0.0197290.0094804 2.1 terminal hydrolase 6 OS = Saccharomyces cerevisiae GN =UBP6 PE = 1 SV = 1 SUR7_YEAST Protein SUR7 SUR7 P54003 34 kDa 8 40.021538 0.010088 2.1 OS = Saccharomyces cerevisiae GN = SUR7 PE = 1 SV= 1 TWF1_YEAST Twinfilin-1 TWF1 P53250 37 kDa 8 4 0.020141 0.0093864 2.1OS = Saccharomyces cerevisiae GN = TWF1 PE = 1 SV = 1 RN49_YEAST 54Sribosomal protein RN49 P40858 18 kDa 6 3 0.026689 0.012968 2.1 L49,mitochondrial OS = Saccharomyces cerevisiae GN = MRPL49 PE = 1 SV = 2RSM28_YEAST 37S ribosomal protein RSM28 Q03430 41 kDa 6 3 0.0140430.0067459 2.1 RSM28, mitochondrial OS = Saccharomyces cerevisiae GN =RSM28 PE = 1 SV = 2

What is claimed is:
 1. A method of identifying proteins, includingproteins comprising posttranslational modifications, specificallyassociated with a target chromatin in a cell, the method comprising: a)providing: i) a first cell sample comprising nucleic acid bindingproteins and the target chromatin and a tag, wherein the targetchromatin is tagged by contacting the target chromatin with a tagcapable of specifically recognizing and binding one or more portions ofthe target chromatin and wherein the tag comprises an affinity handle,and ii) a second cell sample comprising nucleic acid binding proteinsand the target chromatin, wherein the target chromatin is not tagged bycontacting the target chromatin with a non-functional tag that is notcapable of specifically recognizing and binding one or more portions ofthe target chromatin and wherein the non-functional tag comprises anaffinity handle; b) isolating the affinity handle from each cell samplein (a) wherein affinity handle isolated from the first cell sampleconsists of affinity handle bound to tagged target chromatin bound tospecifically associated nucleic acid binding proteins and affinityhandle bound to non-specifically associated nucleic acid bindingproteins and affinity handle isolated from the second cell sampleconsists of affinity handle bound to non-specifically associated nucleicacid binding proteins, wherein isolating the affinity handle enrichesfor the tagged target chromatin; c) identifying bound proteins from (b);and d) determining the amount of each bound protein in each cell samplefrom (b), wherein bound proteins that are enriched in the first cellsample as compared to the second cell sample are specifically associatedwith the tagged chromatin in the first cell sample.
 2. The method ofclaim 1, wherein the tag comprises a nucleic acid engineered to havebinding specificity for a nucleic acid sequence component of the targetchromatin, a protein that associates with the nucleic acid engineered tohave binding specificity for a nucleic acid sequence component of thetarget chromatin, and an affinity handle.
 3. The method of claim 2,wherein the nucleic acid engineered to have binding specificity for anucleic acid sequence component of the target chromatin is a guide RNA(gRNA).
 4. The method of claim 3, wherein the protein that associateswith the gRNA is a nuclease inactivated Cas9 protein, or derivativethereof.
 5. The method of claim 1, wherein the target chromatin in thefirst cell sample is tagged by expressing in a cell a tag comprising anucleic acid engineered to have binding specificity for a nucleic acidsequence component of the target chromatin.
 6. The method of claim 5,wherein the nucleic acid engineered to have binding specificity for anucleic acid sequence component of the target chromatin is a guide RNA.7. The method of claim 1, wherein the target chromatin is tagged byexpressing in a cell a gRNA engineered to have binding specificity for anucleic acid sequence component of the target chromatin, a nucleaseinactivated Cas9 protein that associates with the gRNA, and an affinityhandle.
 8. The method of claim 1, wherein the non-functional tagcomprises a protein capable of associating with a nucleic acidengineered to have binding specificity for a nucleic acid sequencecomponent of the target chromatin and an affinity handle, wherein thenon-functional tag does not comprise a nucleic acid engineered to havebinding specificity for a nucleic acid sequence component of the targetchromatin.
 9. The method of claim 1, wherein the second cell sample iscontacted with a non-functional tag by expressing in a cell a proteincapable of associating with a nucleic acid engineered to have bindingspecificity for a nucleic acid sequence component of the targetchromatin and an affinity handle, wherein the nucleic acid engineered tohave binding specificity for a nucleic acid sequence component of thetarget chromatin is not expressed in the cell.
 10. The method of claim1, wherein the chromatin is fragmented to comprise nucleic acid sectionscomprising 500 to 1500 base pairs.
 11. The method of claim 1, whereinthe target chromatin in the first cell sample is contacted with a tagduring cell culture and the target chromatin in the second cell sampleis contacted with a non-functional tag during cell culture.
 12. Themethod of claim 1, wherein the target chromatin in the first cell sampleis contacted with a tag following cell lysis and the target chromatin inthe second cell sample is contacted with a non-functional tag followingcell lysis.
 13. The method of claim 1, wherein the first and second cellsamples are biological samples.
 14. The method of claim 1, wherein thefirst cell sample and the second cell sample are crosslinked and thenlysed.
 15. The method of claim 1, wherein the affinity handle isisolated using affinity purification.
 16. The method of claim 1, whereinthe identifying of step (c) involves mass spectrometry.
 17. The methodof claim 1, wherein step (d) involves label-free proteomics
 18. Themethod of claim 17, wherein the label-free proteomics technique isspectral counting.
 19. The method of claim 1, wherein proteins enrichedin the first cell sample compared to the second cell sample are enrichedby at least 2 fold.